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### Running command:
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### /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data ISAnalytics
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* checking for file ‘ISAnalytics/DESCRIPTION’ ... OK
* preparing ‘ISAnalytics’:
* checking DESCRIPTION meta-information ... OK
* installing the package to process help pages
* building the PDF package manual
Hmm ... looks like a package
Converting Rd files to LaTeX ......
Creating pdf output from LaTeX ...
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\T1/ptm/m/n/10 group. For more de-tails on how to use this func-tion: \T1/zi4/m
/n/10 vignette("aggregate_function_usage",package
[3]
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\T1/ptm/m/n/10 the spec-i-fied lambda. For more de-tails on how to use this fun
c-tion: \T1/zi4/m/n/10 vignette("aggregate_function_usage",package
[4] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1ptm.fd) [5]
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[]\T1/ptm/m/n/10 Either a sin-gle ma-trix or a list of ma-tri-ces, ide-ally ob-
tained via \T1/zi4/m/n/10 import_parallel_Vispa2Matrices()
[6] [7]
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[]\T1/ptm/m/n/10 Other Util-ity func-tions: [][]\T1/zi4/m/n/10 generate_Vispa2_
launch_AF[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 generate_blank_association
_file[][][]()\T1/ptm/m/n/10 ,
[8] [9]
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[]\T1/ptm/m/n/10 Additional named ar-gu-ments to pass on to cho-sen de-vice, \T
1/zi4/m/n/10 circlize::circos.par()\T1/ptm/m/n/10 ,
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\T1/zi4/m/n/10 circlize::circos.genomicDensity() \T1/ptm/m/n/10 and \T1/zi4/m/n
/10 circlize::circos.genomicLabels()
[10]
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[]\T1/ptm/m/n/10 Other Plot-ting func-tions: [][]\T1/zi4/m/n/10 CIS_volcano_plo
t[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 HSC_population_plot[][][]()\T1/ptm
/m/n/10 , [][]\T1/zi4/m/n/10 integration_alluvial_plot[][][]()\T1/ptm/m/n/10 ,
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\T1/zi4/m/n/10 ashpublications . org / blood / article / 117 / 20 / 5332 / 2120
6 / Lentiviral-[]vector-[]common-[]integration-[]sites-[]in$[][]
[11]
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[]\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 comparison_mat
rix[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm
/m/n/10 , [][]\T1/zi4/m/n/10 cumulative_count_union[][][]()\T1/ptm/m/n/10 ,
[12] [13] (/usr/share/texlive/texmf-dist/tex/latex/inconsolata/ts1zi4.fd)
[14]
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[]\T1/ptm/m/n/10 Other Plot-ting func-tions: [][]\T1/zi4/m/n/10 HSC_population_
plot[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 circos_genomic_density[][][]()\
T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 integration_alluvial_plot[][][]()\T1/ptm/m/n
/10 ,
[15]
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[]\T1/ptm/m/n/10 A named list of in-te-gra-tion ma-tri-ces, ide-ally ob-tained
via [][]im-port_parallel_Vispa2Matrices_interactive[][][]
[16]
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[]\T1/ptm/m/n/10 An in-te-gra-tion ma-trix - aka a data frame that in-cludes th
e \T1/zi4/m/n/10 mandatory_IS_vars()
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\T1/ptm/m/n/10 as columns. The ma-trix can ei-ther be ag-gre-gated (via \T1/zi4
/m/n/10 aggregate_values_by_key()\T1/ptm/m/n/10 )
[17] [18]
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\T1/ptm/m/n/10 data frame con-tains the ref-er-ence of pre-recalibration val-ue
s for \T1/zi4/m/n/10 chr\T1/ptm/m/n/10 , \T1/zi4/m/n/10 strand \T1/ptm/m/n/10 a
nd \T1/zi4/m/n/10 integration_locus
[19] [20]
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[]\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 CIS_grubbs[][]
[]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 comparison_matrix[][][]()\T1/ptm/m/n/10
, [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n
/10 cumulative_is[][][]()\T1/ptm/m/n/10 ,
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[][]\T1/zi4/m/n/10 is_sharing[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 iss_so
urce[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 purity_filter[][][]()\T1/ptm/m/
n/10 , [][]\T1/zi4/m/n/10 sample_statistics[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4
/m/n/10 separate_quant_matrices[][][]()\T1/ptm/m/n/10 ,
[21]
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[]\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 CIS_grubbs[][]
[]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 comparison_matrix[][][]()\T1/ptm/m/n/10
, [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n
/10 cumulative_count_union[][][]()\T1/ptm/m/n/10 ,
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[][]\T1/zi4/m/n/10 is_sharing[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 iss_so
urce[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 purity_filter[][][]()\T1/ptm/m/
n/10 , [][]\T1/zi4/m/n/10 sample_statistics[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4
/m/n/10 separate_quant_matrices[][][]()\T1/ptm/m/n/10 ,
[22]
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[]\T1/ptm/m/it/10 Possible choices for the \T1/zi4/m/n/10 dates_format \T1/ptm/
m/it/10 pa-
Underfull \hbox (badness 10000) in paragraph at lines 1388--1388
\T1/ptm/m/it/10 ram-e-ter in \T1/zi4/m/n/10 import_association_file\T1/ptm/m/it
/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 1388--1388
\T1/zi4/m/n/10 import_parallel_vispa2Matrices_interactive \T1/ptm/m/it/10 and
[23] [24] [25] [26]
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[]\T1/ptm/m/n/10 Other Util-ity func-tions: [][]\T1/zi4/m/n/10 as_sparse_matrix
[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 generate_Vispa2_launch_AF[][][]()\T
1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 unzip_file_system[][][]()
[27]
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[]\T1/ptm/m/n/10 You cor-reclty type names in cor-re-spond-ing po-si-tions, for
ex-am-ple c("CLOEXP", "PROJECT1100",
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[]\T1/ptm/m/n/10 Other Util-ity func-tions: [][]\T1/zi4/m/n/10 as_sparse_matrix
[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 generate_blank_association_file[][]
[]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 unzip_file_system[][][]()
[28]
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[]\T1/ptm/m/n/10 Other Plot-ting func-tions: [][]\T1/zi4/m/n/10 CIS_volcano_plo
t[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 circos_genomic_density[][][]()\T1/
ptm/m/n/10 , [][]\T1/zi4/m/n/10 integration_alluvial_plot[][][]()\T1/ptm/m/n/10
,
[29] [30]
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[]\T1/ptm/m/n/10 The cell types to in-clude in the mod-els. Note that the match
-ing is case-insensitive.
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\T1/ptm/m/n/10 orig-i-nal ma-trix are kept if the se-quence count value is grea
ter or equal than the \T1/zi4/m/n/10 seqCount_threshold
[31] [32]
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\T1/ptm/m/n/10 no re-port should be pro-duced. De-faults to \T1/zi4/m/n/10 {use
r_home}/ISAnalytics_reports\T1/ptm/m/n/10 .
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[]\T1/ptm/m/n/10 Other Im-port func-tions: [][]\T1/zi4/m/n/10 import_Vispa2_sta
ts[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 import_parallel_Vispa2Matrices[][
][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 import_single_Vispa2Matrix[][][]()
[33]
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\T1/ptm/m/n/10 no re-port should be pro-duced. De-faults to \T1/zi4/m/n/10 {use
r_home}/ISAnalytics_reports\T1/ptm/m/n/10 .
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[]\T1/ptm/m/n/10 <[][]\T1/zi4/m/n/10 dynamic-dots[][][]\T1/ptm/m/n/10 > Ad-di-t
ional named ar-gu-ments to pass to \T1/zi4/m/n/10 ìmport_association_file
Overfull \hbox (80.40988pt too wide) in paragraph at lines 2023--2027
[]\T1/ptm/m/n/10 Other Im-port func-tions: [][]\T1/zi4/m/n/10 import_Vispa2_sta
ts[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 import_association_file[][][]()\T
1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 import_single_Vispa2Matrix[][][]()
[34]
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[]\T1/ptm/m/n/10 For more de-tails see the "How to use im-port func-tions" vi-g
nette: \T1/zi4/m/n/10 vignette("import_functions_howto",package
[35]
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[]\T1/ptm/m/n/10 Other Im-port func-tions: [][]\T1/zi4/m/n/10 import_Vispa2_sta
ts[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 import_association_file[][][]()\T
1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 import_parallel_Vispa2Matrices[][][]()
Overfull \hbox (3.81735pt too wide) in paragraph at lines 2143--2146
\T1/ptm/m/n/10 el-e-ments rep-re-sent reg-u-lar ex-pres-sions. For de-faults se
e [][]de-fault_iss_file_prefixes[][][].
[36]
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\T1/ptm/m/n/10 no re-port should be pro-duced. De-faults to \T1/zi4/m/n/10 {use
r_home}/ISAnalytics_reports\T1/ptm/m/n/10 .
[37] [38]
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[]\T1/ptm/m/n/10 Other Plot-ting func-tions: [][]\T1/zi4/m/n/10 CIS_volcano_plo
t[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 HSC_population_plot[][][]()\T1/ptm
/m/n/10 , [][]\T1/zi4/m/n/10 circos_genomic_density[][][]()\T1/ptm/m/n/10 ,
[39]
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[]\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 CIS_grubbs[][]
[]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 comparison_matrix[][][]()\T1/ptm/m/n/10
, [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n
/10 cumulative_count_union[][][]()\T1/ptm/m/n/10 ,
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[][]\T1/zi4/m/n/10 cumulative_is[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 is_
sharing[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 purity_filter[][][]()\T1/ptm
/m/n/10 , [][]\T1/zi4/m/n/10 sample_statistics[][][]()\T1/ptm/m/n/10 , [][]\T1/
zi4/m/n/10 separate_quant_matrices[][][]()\T1/ptm/m/n/10 ,
[40] [41]
Overfull \hbox (122.32698pt too wide) in paragraph at lines 2500--2505
[]\T1/ptm/m/n/10 The func-tion ac-cepts mul-ti-ple in-puts for dif-fer-ent sce-
nar-ios, please re-fer to the vi-gnette \T1/zi4/m/n/10 vignette("sharing_analys
es",package
[42]
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[]\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 CIS_grubbs[][]
[]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 comparison_matrix[][][]()\T1/ptm/m/n/10
, [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n
/10 cumulative_count_union[][][]()\T1/ptm/m/n/10 ,
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[][]\T1/zi4/m/n/10 cumulative_is[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 iss
_source[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 purity_filter[][][]()\T1/ptm
/m/n/10 , [][]\T1/zi4/m/n/10 sample_statistics[][][]()\T1/ptm/m/n/10 , [][]\T1/
zi4/m/n/10 separate_quant_matrices[][][]()\T1/ptm/m/n/10 ,
[43]
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[]\T1/ptm/m/n/10 These are all the pos-si-ble val-ues for the \T1/zi4/m/n/10 ma
tching_opt \T1/ptm/m/n/10 pa-ram-e-ter in \T1/zi4/m/n/10 import_parallel_vispa2
Matrices_auto\T1/ptm/m/n/10 .
[44] [45]
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\T1/ptm/m/n/10 no re-port should be pro-duced. De-faults to \T1/zi4/m/n/10 {use
r_home}/ISAnalytics_reports\T1/ptm/m/n/10 .
[46] [47] [48] [49]
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[]\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 CIS_grubbs[][]
[]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 comparison_matrix[][][]()\T1/ptm/m/n/10
, [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n
/10 cumulative_count_union[][][]()\T1/ptm/m/n/10 ,
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[][]\T1/zi4/m/n/10 cumulative_is[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 is_
sharing[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 iss_source[][][]()\T1/ptm/m/
n/10 , [][]\T1/zi4/m/n/10 sample_statistics[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4
/m/n/10 separate_quant_matrices[][][]()\T1/ptm/m/n/10 ,
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[]\T1/ptm/m/n/10 These are all the pos-si-ble val-ues for the \T1/zi4/m/n/10 qu
antification_type \T1/ptm/m/n/10 pa-ram-e-ter in \T1/zi4/m/n/10 import_parallel
_vispa2Matrices_interactive
[50]
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\T1/ptm/m/n/10 rea-son you re-moved the col-li-sions by pass-ing only the se-qu
ence count ma-trix to \T1/zi4/m/n/10 remove_collisions()\T1/ptm/m/n/10 ,
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[]\T1/ptm/m/n/10 The se-quence count ma-trix al-ready pro-cessed for col-li-sio
ns via \T1/zi4/m/n/10 remove_collisions()
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[]\T1/ptm/m/n/10 For more de-tails on how to use col-li-sion re-moval func-tion
-al-ity: \T1/zi4/m/n/10 vignette("collision_removal",package
[51] [52] (/usr/share/texlive/texmf-dist/tex/latex/base/t1cmtt.fd)
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\T1/ptm/m/n/10 tails re-fer to the vi-gnette "Col-li-sion re-moval func-tion-al
-ity": \T1/zi4/m/n/10 vignette("collision_removal",package
[54]
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[]\T1/ptm/m/n/10 The date col-umn that should be con-sid-ered. Must be one valu
e in \T1/zi4/m/n/10 date_columns_coll()
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\T1/ptm/m/n/10 no re-port should be pro-duced. De-faults to \T1/zi4/m/n/10 {use
r_home}/ISAnalytics_reports\T1/ptm/m/n/10 .
[55]
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[]\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 CIS_grubbs[][]
[]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 comparison_matrix[][][]()\T1/ptm/m/n/10
, [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n
/10 cumulative_count_union[][][]()\T1/ptm/m/n/10 ,
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[][]\T1/zi4/m/n/10 cumulative_is[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 is_
sharing[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 iss_source[][][]()\T1/ptm/m/
n/10 , [][]\T1/zi4/m/n/10 purity_filter[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n
/10 separate_quant_matrices[][][]()\T1/ptm/m/n/10 ,
[56] [57]
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[]\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 CIS_grubbs[][]
[]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 comparison_matrix[][][]()\T1/ptm/m/n/10
, [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n
/10 cumulative_count_union[][][]()\T1/ptm/m/n/10 ,
[58]
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[]\T1/ptm/m/n/10 Other Plot-ting func-tions: [][]\T1/zi4/m/n/10 CIS_volcano_plo
t[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 HSC_population_plot[][][]()\T1/ptm
/m/n/10 , [][]\T1/zi4/m/n/10 circos_genomic_density[][][]()\T1/ptm/m/n/10 ,
[59]
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[]\T1/ptm/m/n/10 Other Plot-ting func-tions: [][]\T1/zi4/m/n/10 CIS_volcano_plo
t[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 HSC_population_plot[][][]()\T1/ptm
/m/n/10 , [][]\T1/zi4/m/n/10 circos_genomic_density[][][]()\T1/ptm/m/n/10 ,
[60]
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\T1/ptm/m/n/10 nu-meric vec-tor for \T1/zi4/m/n/10 threshold \T1/ptm/m/n/10 and
char-ac-ter vec-tors for both \T1/zi4/m/n/10 cols_to_compare \T1/ptm/m/n/10 an
d \T1/zi4/m/n/10 comparators\T1/ptm/m/n/10 .
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\T1/ptm/m/n/10 A fil-ter-ing con-di-tion is ob-tained by com-bin-ing el-e-ment
by el-e-ment \T1/zi4/m/n/10 cols_to_compare \T1/ptm/m/n/10 + \T1/zi4/m/n/10 com
parators
[61] [62]
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[]\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 CIS_grubbs[][]
[]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 comparison_matrix[][][]()\T1/ptm/m/n/10
, [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n
/10 cumulative_count_union[][][]()\T1/ptm/m/n/10 ,
[63] [64]
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[]\T1/ptm/m/n/10 Other Plot-ting func-tions: [][]\T1/zi4/m/n/10 CIS_volcano_plo
t[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 HSC_population_plot[][][]()\T1/ptm
/m/n/10 , [][]\T1/zi4/m/n/10 circos_genomic_density[][][]()\T1/ptm/m/n/10 ,
[65]
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[]\T1/zi4/m/n/10 keep = "nothing" \T1/ptm/m/n/10 only keeps the manda-tory colu
mns (\T1/zi4/m/n/10 mandatory_IS_vars()\T1/ptm/m/n/10 ) plus the columns
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[]\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 CIS_grubbs[][]
[]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 comparison_matrix[][][]()\T1/ptm/m/n/10
, [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n
/10 cumulative_count_union[][][]()\T1/ptm/m/n/10 ,
[66]
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[]\T1/ptm/m/n/10 Other Util-ity func-tions: [][]\T1/zi4/m/n/10 as_sparse_matrix
[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 generate_Vispa2_launch_AF[][][]()\T
1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 generate_blank_association_file[][][]()
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[2] [3])
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\T1/ptm/m/n/10 group. For more de-tails on how to use this func-tion: \T1/zi4/m
/n/10 vignette("aggregate_function_usage",package
[4]
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\T1/ptm/m/n/10 the spec-i-fied lambda. For more de-tails on how to use this fun
c-tion: \T1/zi4/m/n/10 vignette("aggregate_function_usage",package
[5] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1ptm.fd) [6]
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[]\T1/ptm/m/n/10 Either a sin-gle ma-trix or a list of ma-tri-ces, ide-ally ob-
tained via \T1/zi4/m/n/10 import_parallel_Vispa2Matrices()
[7] [8]
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[]\T1/ptm/m/n/10 Other Util-ity func-tions: [][]\T1/zi4/m/n/10 generate_Vispa2_
launch_AF[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 generate_blank_association
_file[][][]()\T1/ptm/m/n/10 ,
[9] [10]
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[]\T1/ptm/m/n/10 Additional named ar-gu-ments to pass on to cho-sen de-vice, \T
1/zi4/m/n/10 circlize::circos.par()\T1/ptm/m/n/10 ,
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\T1/zi4/m/n/10 circlize::circos.genomicDensity() \T1/ptm/m/n/10 and \T1/zi4/m/n
/10 circlize::circos.genomicLabels()
[11]
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[]\T1/ptm/m/n/10 Other Plot-ting func-tions: [][]\T1/zi4/m/n/10 CIS_volcano_plo
t[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 HSC_population_plot[][][]()\T1/ptm
/m/n/10 , [][]\T1/zi4/m/n/10 integration_alluvial_plot[][][]()\T1/ptm/m/n/10 ,
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\T1/zi4/m/n/10 ashpublications . org / blood / article / 117 / 20 / 5332 / 2120
6 / Lentiviral-[]vector-[]common-[]integration-[]sites-[]in$[][]
[12]
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[]\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 comparison_mat
rix[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm
/m/n/10 , [][]\T1/zi4/m/n/10 cumulative_count_union[][][]()\T1/ptm/m/n/10 ,
[13] [14] (/usr/share/texlive/texmf-dist/tex/latex/inconsolata/ts1zi4.fd)
[15]
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[]\T1/ptm/m/n/10 Other Plot-ting func-tions: [][]\T1/zi4/m/n/10 HSC_population_
plot[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 circos_genomic_density[][][]()\
T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 integration_alluvial_plot[][][]()\T1/ptm/m/n
/10 ,
[16]
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[]\T1/ptm/m/n/10 A named list of in-te-gra-tion ma-tri-ces, ide-ally ob-tained
via [][]im-port_parallel_Vispa2Matrices_interactive[][][]
[17]
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[]\T1/ptm/m/n/10 An in-te-gra-tion ma-trix - aka a data frame that in-cludes th
e \T1/zi4/m/n/10 mandatory_IS_vars()
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\T1/ptm/m/n/10 as columns. The ma-trix can ei-ther be ag-gre-gated (via \T1/zi4
/m/n/10 aggregate_values_by_key()\T1/ptm/m/n/10 )
[18] [19]
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\T1/ptm/m/n/10 data frame con-tains the ref-er-ence of pre-recalibration val-ue
s for \T1/zi4/m/n/10 chr\T1/ptm/m/n/10 , \T1/zi4/m/n/10 strand \T1/ptm/m/n/10 a
nd \T1/zi4/m/n/10 integration_locus
[20] [21]
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[]\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 CIS_grubbs[][]
[]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 comparison_matrix[][][]()\T1/ptm/m/n/10
, [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n
/10 cumulative_is[][][]()\T1/ptm/m/n/10 ,
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[][]\T1/zi4/m/n/10 is_sharing[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 iss_so
urce[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 purity_filter[][][]()\T1/ptm/m/
n/10 , [][]\T1/zi4/m/n/10 sample_statistics[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4
/m/n/10 separate_quant_matrices[][][]()\T1/ptm/m/n/10 ,
[22]
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[]\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 CIS_grubbs[][]
[]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 comparison_matrix[][][]()\T1/ptm/m/n/10
, [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n
/10 cumulative_count_union[][][]()\T1/ptm/m/n/10 ,
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[][]\T1/zi4/m/n/10 is_sharing[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 iss_so
urce[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 purity_filter[][][]()\T1/ptm/m/
n/10 , [][]\T1/zi4/m/n/10 sample_statistics[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4
/m/n/10 separate_quant_matrices[][][]()\T1/ptm/m/n/10 ,
[23]
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[]\T1/ptm/m/it/10 Possible choices for the \T1/zi4/m/n/10 dates_format \T1/ptm/
m/it/10 pa-
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\T1/ptm/m/it/10 ram-e-ter in \T1/zi4/m/n/10 import_association_file\T1/ptm/m/it
/10 ,
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\T1/zi4/m/n/10 import_parallel_vispa2Matrices_interactive \T1/ptm/m/it/10 and
[24] [25] [26] [27]
Overfull \hbox (29.30962pt too wide) in paragraph at lines 1573--1577
[]\T1/ptm/m/n/10 Other Util-ity func-tions: [][]\T1/zi4/m/n/10 as_sparse_matrix
[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 generate_Vispa2_launch_AF[][][]()\T
1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 unzip_file_system[][][]()
[28]
Overfull \hbox (19.25786pt too wide) in paragraph at lines 1624--1629
[]\T1/ptm/m/n/10 You cor-reclty type names in cor-re-spond-ing po-si-tions, for
ex-am-ple c("CLOEXP", "PROJECT1100",
Overfull \hbox (59.30962pt too wide) in paragraph at lines 1639--1643
[]\T1/ptm/m/n/10 Other Util-ity func-tions: [][]\T1/zi4/m/n/10 as_sparse_matrix
[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 generate_blank_association_file[][]
[]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 unzip_file_system[][][]()
[29]
Overfull \hbox (62.36969pt too wide) in paragraph at lines 1691--1698
[]\T1/ptm/m/n/10 Other Plot-ting func-tions: [][]\T1/zi4/m/n/10 CIS_volcano_plo
t[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 circos_genomic_density[][][]()\T1/
ptm/m/n/10 , [][]\T1/zi4/m/n/10 integration_alluvial_plot[][][]()\T1/ptm/m/n/10
,
[30] [31]
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[]\T1/ptm/m/n/10 The cell types to in-clude in the mod-els. Note that the match
-ing is case-insensitive.
Overfull \hbox (2.29784pt too wide) in paragraph at lines 1822--1831
\T1/ptm/m/n/10 orig-i-nal ma-trix are kept if the se-quence count value is grea
ter or equal than the \T1/zi4/m/n/10 seqCount_threshold
[32] [33]
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\T1/ptm/m/n/10 no re-port should be pro-duced. De-faults to \T1/zi4/m/n/10 {use
r_home}/ISAnalytics_reports\T1/ptm/m/n/10 .
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[]\T1/ptm/m/n/10 Other Im-port func-tions: [][]\T1/zi4/m/n/10 import_Vispa2_sta
ts[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 import_parallel_Vispa2Matrices[][
][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 import_single_Vispa2Matrix[][][]()
[34]
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\T1/ptm/m/n/10 no re-port should be pro-duced. De-faults to \T1/zi4/m/n/10 {use
r_home}/ISAnalytics_reports\T1/ptm/m/n/10 .
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[]\T1/ptm/m/n/10 <[][]\T1/zi4/m/n/10 dynamic-dots[][][]\T1/ptm/m/n/10 > Ad-di-t
ional named ar-gu-ments to pass to \T1/zi4/m/n/10 ìmport_association_file
Overfull \hbox (80.40988pt too wide) in paragraph at lines 2023--2027
[]\T1/ptm/m/n/10 Other Im-port func-tions: [][]\T1/zi4/m/n/10 import_Vispa2_sta
ts[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 import_association_file[][][]()\T
1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 import_single_Vispa2Matrix[][][]()
[35]
Overfull \hbox (64.31819pt too wide) in paragraph at lines 2085--2087
[]\T1/ptm/m/n/10 For more de-tails see the "How to use im-port func-tions" vi-g
nette: \T1/zi4/m/n/10 vignette("import_functions_howto",package
[36]
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[]\T1/ptm/m/n/10 Other Im-port func-tions: [][]\T1/zi4/m/n/10 import_Vispa2_sta
ts[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 import_association_file[][][]()\T
1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 import_parallel_Vispa2Matrices[][][]()
Overfull \hbox (3.81735pt too wide) in paragraph at lines 2143--2146
\T1/ptm/m/n/10 el-e-ments rep-re-sent reg-u-lar ex-pres-sions. For de-faults se
e [][]de-fault_iss_file_prefixes[][][].
[37]
Overfull \hbox (5.10971pt too wide) in paragraph at lines 2155--2158
\T1/ptm/m/n/10 no re-port should be pro-duced. De-faults to \T1/zi4/m/n/10 {use
r_home}/ISAnalytics_reports\T1/ptm/m/n/10 .
[38] [39]
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[]\T1/ptm/m/n/10 Other Plot-ting func-tions: [][]\T1/zi4/m/n/10 CIS_volcano_plo
t[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 HSC_population_plot[][][]()\T1/ptm
/m/n/10 , [][]\T1/zi4/m/n/10 circos_genomic_density[][][]()\T1/ptm/m/n/10 ,
[40]
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[]\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 CIS_grubbs[][]
[]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 comparison_matrix[][][]()\T1/ptm/m/n/10
, [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n
/10 cumulative_count_union[][][]()\T1/ptm/m/n/10 ,
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[][]\T1/zi4/m/n/10 cumulative_is[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 is_
sharing[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 purity_filter[][][]()\T1/ptm
/m/n/10 , [][]\T1/zi4/m/n/10 sample_statistics[][][]()\T1/ptm/m/n/10 , [][]\T1/
zi4/m/n/10 separate_quant_matrices[][][]()\T1/ptm/m/n/10 ,
[41] [42]
Overfull \hbox (122.32698pt too wide) in paragraph at lines 2500--2505
[]\T1/ptm/m/n/10 The func-tion ac-cepts mul-ti-ple in-puts for dif-fer-ent sce-
nar-ios, please re-fer to the vi-gnette \T1/zi4/m/n/10 vignette("sharing_analys
es",package
[43]
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[]\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 CIS_grubbs[][]
[]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 comparison_matrix[][][]()\T1/ptm/m/n/10
, [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n
/10 cumulative_count_union[][][]()\T1/ptm/m/n/10 ,
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[][]\T1/zi4/m/n/10 cumulative_is[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 iss
_source[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 purity_filter[][][]()\T1/ptm
/m/n/10 , [][]\T1/zi4/m/n/10 sample_statistics[][][]()\T1/ptm/m/n/10 , [][]\T1/
zi4/m/n/10 separate_quant_matrices[][][]()\T1/ptm/m/n/10 ,
[44]
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[]\T1/ptm/m/n/10 These are all the pos-si-ble val-ues for the \T1/zi4/m/n/10 ma
tching_opt \T1/ptm/m/n/10 pa-ram-e-ter in \T1/zi4/m/n/10 import_parallel_vispa2
Matrices_auto\T1/ptm/m/n/10 .
[45] [46]
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\T1/ptm/m/n/10 no re-port should be pro-duced. De-faults to \T1/zi4/m/n/10 {use
r_home}/ISAnalytics_reports\T1/ptm/m/n/10 .
[47] [48] [49] [50]
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[]\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 CIS_grubbs[][]
[]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 comparison_matrix[][][]()\T1/ptm/m/n/10
, [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n
/10 cumulative_count_union[][][]()\T1/ptm/m/n/10 ,
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[][]\T1/zi4/m/n/10 cumulative_is[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 is_
sharing[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 iss_source[][][]()\T1/ptm/m/
n/10 , [][]\T1/zi4/m/n/10 sample_statistics[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4
/m/n/10 separate_quant_matrices[][][]()\T1/ptm/m/n/10 ,
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[]\T1/ptm/m/n/10 These are all the pos-si-ble val-ues for the \T1/zi4/m/n/10 qu
antification_type \T1/ptm/m/n/10 pa-ram-e-ter in \T1/zi4/m/n/10 import_parallel
_vispa2Matrices_interactive
[51]
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\T1/ptm/m/n/10 rea-son you re-moved the col-li-sions by pass-ing only the se-qu
ence count ma-trix to \T1/zi4/m/n/10 remove_collisions()\T1/ptm/m/n/10 ,
Overfull \hbox (25.75836pt too wide) in paragraph at lines 3074--3076
[]\T1/ptm/m/n/10 The se-quence count ma-trix al-ready pro-cessed for col-li-sio
ns via \T1/zi4/m/n/10 remove_collisions()
Overfull \hbox (33.86833pt too wide) in paragraph at lines 3084--3086
[]\T1/ptm/m/n/10 For more de-tails on how to use col-li-sion re-moval func-tion
-al-ity: \T1/zi4/m/n/10 vignette("collision_removal",package
[52] [53] (/usr/share/texlive/texmf-dist/tex/latex/base/t1cmtt.fd)
(/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmtt.fd) [54]
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\T1/ptm/m/n/10 tails re-fer to the vi-gnette "Col-li-sion re-moval func-tion-al
-ity": \T1/zi4/m/n/10 vignette("collision_removal",package
[55]
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[]\T1/ptm/m/n/10 The date col-umn that should be con-sid-ered. Must be one valu
e in \T1/zi4/m/n/10 date_columns_coll()
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\T1/ptm/m/n/10 no re-port should be pro-duced. De-faults to \T1/zi4/m/n/10 {use
r_home}/ISAnalytics_reports\T1/ptm/m/n/10 .
[56]
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[]\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 CIS_grubbs[][]
[]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 comparison_matrix[][][]()\T1/ptm/m/n/10
, [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n
/10 cumulative_count_union[][][]()\T1/ptm/m/n/10 ,
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[][]\T1/zi4/m/n/10 cumulative_is[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 is_
sharing[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 iss_source[][][]()\T1/ptm/m/
n/10 , [][]\T1/zi4/m/n/10 purity_filter[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n
/10 separate_quant_matrices[][][]()\T1/ptm/m/n/10 ,
[57] [58]
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[]\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 CIS_grubbs[][]
[]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 comparison_matrix[][][]()\T1/ptm/m/n/10
, [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n
/10 cumulative_count_union[][][]()\T1/ptm/m/n/10 ,
[59]
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[]\T1/ptm/m/n/10 Other Plot-ting func-tions: [][]\T1/zi4/m/n/10 CIS_volcano_plo
t[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 HSC_population_plot[][][]()\T1/ptm
/m/n/10 , [][]\T1/zi4/m/n/10 circos_genomic_density[][][]()\T1/ptm/m/n/10 ,
[60]
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[]\T1/ptm/m/n/10 Other Plot-ting func-tions: [][]\T1/zi4/m/n/10 CIS_volcano_plo
t[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 HSC_population_plot[][][]()\T1/ptm
/m/n/10 , [][]\T1/zi4/m/n/10 circos_genomic_density[][][]()\T1/ptm/m/n/10 ,
[61]
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\T1/ptm/m/n/10 nu-meric vec-tor for \T1/zi4/m/n/10 threshold \T1/ptm/m/n/10 and
char-ac-ter vec-tors for both \T1/zi4/m/n/10 cols_to_compare \T1/ptm/m/n/10 an
d \T1/zi4/m/n/10 comparators\T1/ptm/m/n/10 .
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\T1/ptm/m/n/10 A fil-ter-ing con-di-tion is ob-tained by com-bin-ing el-e-ment
by el-e-ment \T1/zi4/m/n/10 cols_to_compare \T1/ptm/m/n/10 + \T1/zi4/m/n/10 com
parators
[62] [63]
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[]\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 CIS_grubbs[][]
[]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 comparison_matrix[][][]()\T1/ptm/m/n/10
, [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n
/10 cumulative_count_union[][][]()\T1/ptm/m/n/10 ,
[64] [65]
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[]\T1/ptm/m/n/10 Other Plot-ting func-tions: [][]\T1/zi4/m/n/10 CIS_volcano_plo
t[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 HSC_population_plot[][][]()\T1/ptm
/m/n/10 , [][]\T1/zi4/m/n/10 circos_genomic_density[][][]()\T1/ptm/m/n/10 ,
[66]
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[]\T1/zi4/m/n/10 keep = "nothing" \T1/ptm/m/n/10 only keeps the manda-tory colu
mns (\T1/zi4/m/n/10 mandatory_IS_vars()\T1/ptm/m/n/10 ) plus the columns
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[]\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 CIS_grubbs[][]
[]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 comparison_matrix[][][]()\T1/ptm/m/n/10
, [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n
/10 cumulative_count_union[][][]()\T1/ptm/m/n/10 ,
[67]
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[]\T1/ptm/m/n/10 Other Util-ity func-tions: [][]\T1/zi4/m/n/10 as_sparse_matrix
[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 generate_Vispa2_launch_AF[][][]()\T
1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 generate_blank_association_file[][][]()
[68]
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[2] [3])
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\T1/ptm/m/n/10 group. For more de-tails on how to use this func-tion: \T1/zi4/m
/n/10 vignette("aggregate_function_usage",package
[4]
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\T1/ptm/m/n/10 the spec-i-fied lambda. For more de-tails on how to use this fun
c-tion: \T1/zi4/m/n/10 vignette("aggregate_function_usage",package
[5] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1ptm.fd) [6]
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[]\T1/ptm/m/n/10 Either a sin-gle ma-trix or a list of ma-tri-ces, ide-ally ob-
tained via \T1/zi4/m/n/10 import_parallel_Vispa2Matrices()
[7] [8]
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[]\T1/ptm/m/n/10 Other Util-ity func-tions: [][]\T1/zi4/m/n/10 generate_Vispa2_
launch_AF[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 generate_blank_association
_file[][][]()\T1/ptm/m/n/10 ,
[9] [10]
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[]\T1/ptm/m/n/10 Additional named ar-gu-ments to pass on to cho-sen de-vice, \T
1/zi4/m/n/10 circlize::circos.par()\T1/ptm/m/n/10 ,
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\T1/zi4/m/n/10 circlize::circos.genomicDensity() \T1/ptm/m/n/10 and \T1/zi4/m/n
/10 circlize::circos.genomicLabels()
[11]
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[]\T1/ptm/m/n/10 Other Plot-ting func-tions: [][]\T1/zi4/m/n/10 CIS_volcano_plo
t[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 HSC_population_plot[][][]()\T1/ptm
/m/n/10 , [][]\T1/zi4/m/n/10 integration_alluvial_plot[][][]()\T1/ptm/m/n/10 ,
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\T1/zi4/m/n/10 ashpublications . org / blood / article / 117 / 20 / 5332 / 2120
6 / Lentiviral-[]vector-[]common-[]integration-[]sites-[]in$[][]
[12]
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[]\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 comparison_mat
rix[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm
/m/n/10 , [][]\T1/zi4/m/n/10 cumulative_count_union[][][]()\T1/ptm/m/n/10 ,
[13] [14] (/usr/share/texlive/texmf-dist/tex/latex/inconsolata/ts1zi4.fd)
[15]
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[]\T1/ptm/m/n/10 Other Plot-ting func-tions: [][]\T1/zi4/m/n/10 HSC_population_
plot[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 circos_genomic_density[][][]()\
T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 integration_alluvial_plot[][][]()\T1/ptm/m/n
/10 ,
[16]
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[]\T1/ptm/m/n/10 A named list of in-te-gra-tion ma-tri-ces, ide-ally ob-tained
via [][]im-port_parallel_Vispa2Matrices_interactive[][][]
[17]
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[]\T1/ptm/m/n/10 An in-te-gra-tion ma-trix - aka a data frame that in-cludes th
e \T1/zi4/m/n/10 mandatory_IS_vars()
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\T1/ptm/m/n/10 as columns. The ma-trix can ei-ther be ag-gre-gated (via \T1/zi4
/m/n/10 aggregate_values_by_key()\T1/ptm/m/n/10 )
[18] [19]
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\T1/ptm/m/n/10 data frame con-tains the ref-er-ence of pre-recalibration val-ue
s for \T1/zi4/m/n/10 chr\T1/ptm/m/n/10 , \T1/zi4/m/n/10 strand \T1/ptm/m/n/10 a
nd \T1/zi4/m/n/10 integration_locus
[20] [21]
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[]\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 CIS_grubbs[][]
[]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 comparison_matrix[][][]()\T1/ptm/m/n/10
, [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n
/10 cumulative_is[][][]()\T1/ptm/m/n/10 ,
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[][]\T1/zi4/m/n/10 is_sharing[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 iss_so
urce[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 purity_filter[][][]()\T1/ptm/m/
n/10 , [][]\T1/zi4/m/n/10 sample_statistics[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4
/m/n/10 separate_quant_matrices[][][]()\T1/ptm/m/n/10 ,
[22]
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[]\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 CIS_grubbs[][]
[]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 comparison_matrix[][][]()\T1/ptm/m/n/10
, [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n
/10 cumulative_count_union[][][]()\T1/ptm/m/n/10 ,
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[][]\T1/zi4/m/n/10 is_sharing[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 iss_so
urce[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 purity_filter[][][]()\T1/ptm/m/
n/10 , [][]\T1/zi4/m/n/10 sample_statistics[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4
/m/n/10 separate_quant_matrices[][][]()\T1/ptm/m/n/10 ,
[23]
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[]\T1/ptm/m/it/10 Possible choices for the \T1/zi4/m/n/10 dates_format \T1/ptm/
m/it/10 pa-
Underfull \hbox (badness 10000) in paragraph at lines 1388--1388
\T1/ptm/m/it/10 ram-e-ter in \T1/zi4/m/n/10 import_association_file\T1/ptm/m/it
/10 ,
Underfull \hbox (badness 10000) in paragraph at lines 1388--1388
\T1/zi4/m/n/10 import_parallel_vispa2Matrices_interactive \T1/ptm/m/it/10 and
[24] [25] [26] [27]
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[]\T1/ptm/m/n/10 Other Util-ity func-tions: [][]\T1/zi4/m/n/10 as_sparse_matrix
[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 generate_Vispa2_launch_AF[][][]()\T
1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 unzip_file_system[][][]()
[28]
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[]\T1/ptm/m/n/10 You cor-reclty type names in cor-re-spond-ing po-si-tions, for
ex-am-ple c("CLOEXP", "PROJECT1100",
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[]\T1/ptm/m/n/10 Other Util-ity func-tions: [][]\T1/zi4/m/n/10 as_sparse_matrix
[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 generate_blank_association_file[][]
[]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 unzip_file_system[][][]()
[29]
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[]\T1/ptm/m/n/10 Other Plot-ting func-tions: [][]\T1/zi4/m/n/10 CIS_volcano_plo
t[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 circos_genomic_density[][][]()\T1/
ptm/m/n/10 , [][]\T1/zi4/m/n/10 integration_alluvial_plot[][][]()\T1/ptm/m/n/10
,
[30] [31]
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[]\T1/ptm/m/n/10 The cell types to in-clude in the mod-els. Note that the match
-ing is case-insensitive.
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\T1/ptm/m/n/10 orig-i-nal ma-trix are kept if the se-quence count value is grea
ter or equal than the \T1/zi4/m/n/10 seqCount_threshold
[32] [33]
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\T1/ptm/m/n/10 no re-port should be pro-duced. De-faults to \T1/zi4/m/n/10 {use
r_home}/ISAnalytics_reports\T1/ptm/m/n/10 .
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[]\T1/ptm/m/n/10 Other Im-port func-tions: [][]\T1/zi4/m/n/10 import_Vispa2_sta
ts[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 import_parallel_Vispa2Matrices[][
][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 import_single_Vispa2Matrix[][][]()
[34]
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\T1/ptm/m/n/10 no re-port should be pro-duced. De-faults to \T1/zi4/m/n/10 {use
r_home}/ISAnalytics_reports\T1/ptm/m/n/10 .
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[]\T1/ptm/m/n/10 <[][]\T1/zi4/m/n/10 dynamic-dots[][][]\T1/ptm/m/n/10 > Ad-di-t
ional named ar-gu-ments to pass to \T1/zi4/m/n/10 ìmport_association_file
Overfull \hbox (80.40988pt too wide) in paragraph at lines 2023--2027
[]\T1/ptm/m/n/10 Other Im-port func-tions: [][]\T1/zi4/m/n/10 import_Vispa2_sta
ts[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 import_association_file[][][]()\T
1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 import_single_Vispa2Matrix[][][]()
[35]
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[]\T1/ptm/m/n/10 For more de-tails see the "How to use im-port func-tions" vi-g
nette: \T1/zi4/m/n/10 vignette("import_functions_howto",package
[36]
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[]\T1/ptm/m/n/10 Other Im-port func-tions: [][]\T1/zi4/m/n/10 import_Vispa2_sta
ts[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 import_association_file[][][]()\T
1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 import_parallel_Vispa2Matrices[][][]()
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\T1/ptm/m/n/10 el-e-ments rep-re-sent reg-u-lar ex-pres-sions. For de-faults se
e [][]de-fault_iss_file_prefixes[][][].
[37]
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\T1/ptm/m/n/10 no re-port should be pro-duced. De-faults to \T1/zi4/m/n/10 {use
r_home}/ISAnalytics_reports\T1/ptm/m/n/10 .
[38] [39]
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[]\T1/ptm/m/n/10 Other Plot-ting func-tions: [][]\T1/zi4/m/n/10 CIS_volcano_plo
t[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 HSC_population_plot[][][]()\T1/ptm
/m/n/10 , [][]\T1/zi4/m/n/10 circos_genomic_density[][][]()\T1/ptm/m/n/10 ,
[40]
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[]\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 CIS_grubbs[][]
[]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 comparison_matrix[][][]()\T1/ptm/m/n/10
, [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n
/10 cumulative_count_union[][][]()\T1/ptm/m/n/10 ,
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[][]\T1/zi4/m/n/10 cumulative_is[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 is_
sharing[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 purity_filter[][][]()\T1/ptm
/m/n/10 , [][]\T1/zi4/m/n/10 sample_statistics[][][]()\T1/ptm/m/n/10 , [][]\T1/
zi4/m/n/10 separate_quant_matrices[][][]()\T1/ptm/m/n/10 ,
[41] [42]
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[]\T1/ptm/m/n/10 The func-tion ac-cepts mul-ti-ple in-puts for dif-fer-ent sce-
nar-ios, please re-fer to the vi-gnette \T1/zi4/m/n/10 vignette("sharing_analys
es",package
[43]
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[]\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 CIS_grubbs[][]
[]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 comparison_matrix[][][]()\T1/ptm/m/n/10
, [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n
/10 cumulative_count_union[][][]()\T1/ptm/m/n/10 ,
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[][]\T1/zi4/m/n/10 cumulative_is[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 iss
_source[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 purity_filter[][][]()\T1/ptm
/m/n/10 , [][]\T1/zi4/m/n/10 sample_statistics[][][]()\T1/ptm/m/n/10 , [][]\T1/
zi4/m/n/10 separate_quant_matrices[][][]()\T1/ptm/m/n/10 ,
[44]
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[]\T1/ptm/m/n/10 These are all the pos-si-ble val-ues for the \T1/zi4/m/n/10 ma
tching_opt \T1/ptm/m/n/10 pa-ram-e-ter in \T1/zi4/m/n/10 import_parallel_vispa2
Matrices_auto\T1/ptm/m/n/10 .
[45] [46]
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\T1/ptm/m/n/10 no re-port should be pro-duced. De-faults to \T1/zi4/m/n/10 {use
r_home}/ISAnalytics_reports\T1/ptm/m/n/10 .
[47] [48] [49] [50]
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[]\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 CIS_grubbs[][]
[]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 comparison_matrix[][][]()\T1/ptm/m/n/10
, [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n
/10 cumulative_count_union[][][]()\T1/ptm/m/n/10 ,
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[][]\T1/zi4/m/n/10 cumulative_is[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 is_
sharing[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 iss_source[][][]()\T1/ptm/m/
n/10 , [][]\T1/zi4/m/n/10 sample_statistics[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4
/m/n/10 separate_quant_matrices[][][]()\T1/ptm/m/n/10 ,
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[]\T1/ptm/m/n/10 These are all the pos-si-ble val-ues for the \T1/zi4/m/n/10 qu
antification_type \T1/ptm/m/n/10 pa-ram-e-ter in \T1/zi4/m/n/10 import_parallel
_vispa2Matrices_interactive
[51]
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\T1/ptm/m/n/10 rea-son you re-moved the col-li-sions by pass-ing only the se-qu
ence count ma-trix to \T1/zi4/m/n/10 remove_collisions()\T1/ptm/m/n/10 ,
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[]\T1/ptm/m/n/10 The se-quence count ma-trix al-ready pro-cessed for col-li-sio
ns via \T1/zi4/m/n/10 remove_collisions()
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[]\T1/ptm/m/n/10 For more de-tails on how to use col-li-sion re-moval func-tion
-al-ity: \T1/zi4/m/n/10 vignette("collision_removal",package
[52] [53] (/usr/share/texlive/texmf-dist/tex/latex/base/t1cmtt.fd)
(/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmtt.fd) [54]
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\T1/ptm/m/n/10 tails re-fer to the vi-gnette "Col-li-sion re-moval func-tion-al
-ity": \T1/zi4/m/n/10 vignette("collision_removal",package
[55]
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[]\T1/ptm/m/n/10 The date col-umn that should be con-sid-ered. Must be one valu
e in \T1/zi4/m/n/10 date_columns_coll()
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\T1/ptm/m/n/10 no re-port should be pro-duced. De-faults to \T1/zi4/m/n/10 {use
r_home}/ISAnalytics_reports\T1/ptm/m/n/10 .
[56]
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[]\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 CIS_grubbs[][]
[]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 comparison_matrix[][][]()\T1/ptm/m/n/10
, [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n
/10 cumulative_count_union[][][]()\T1/ptm/m/n/10 ,
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[][]\T1/zi4/m/n/10 cumulative_is[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 is_
sharing[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 iss_source[][][]()\T1/ptm/m/
n/10 , [][]\T1/zi4/m/n/10 purity_filter[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n
/10 separate_quant_matrices[][][]()\T1/ptm/m/n/10 ,
[57] [58]
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[]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 comparison_matrix[][][]()\T1/ptm/m/n/10
, [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n
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[59]
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t[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 HSC_population_plot[][][]()\T1/ptm
/m/n/10 , [][]\T1/zi4/m/n/10 circos_genomic_density[][][]()\T1/ptm/m/n/10 ,
[60]
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t[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 HSC_population_plot[][][]()\T1/ptm
/m/n/10 , [][]\T1/zi4/m/n/10 circos_genomic_density[][][]()\T1/ptm/m/n/10 ,
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\T1/ptm/m/n/10 nu-meric vec-tor for \T1/zi4/m/n/10 threshold \T1/ptm/m/n/10 and
char-ac-ter vec-tors for both \T1/zi4/m/n/10 cols_to_compare \T1/ptm/m/n/10 an
d \T1/zi4/m/n/10 comparators\T1/ptm/m/n/10 .
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\T1/ptm/m/n/10 A fil-ter-ing con-di-tion is ob-tained by com-bin-ing el-e-ment
by el-e-ment \T1/zi4/m/n/10 cols_to_compare \T1/ptm/m/n/10 + \T1/zi4/m/n/10 com
parators
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[]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 comparison_matrix[][][]()\T1/ptm/m/n/10
, [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n
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t[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 HSC_population_plot[][][]()\T1/ptm
/m/n/10 , [][]\T1/zi4/m/n/10 circos_genomic_density[][][]()\T1/ptm/m/n/10 ,
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, [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n
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[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 generate_Vispa2_launch_AF[][][]()\T
1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 generate_blank_association_file[][][]()
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\T1/ptm/m/n/10 group. For more de-tails on how to use this func-tion: \T1/zi4/m
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[]\T1/ptm/m/n/10 Either a sin-gle ma-trix or a list of ma-tri-ces, ide-ally ob-
tained via \T1/zi4/m/n/10 import_parallel_Vispa2Matrices()
[7] [8]
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[]\T1/ptm/m/n/10 Other Util-ity func-tions: [][]\T1/zi4/m/n/10 generate_Vispa2_
launch_AF[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 generate_blank_association
_file[][][]()\T1/ptm/m/n/10 ,
[9] [10]
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[]\T1/ptm/m/n/10 Additional named ar-gu-ments to pass on to cho-sen de-vice, \T
1/zi4/m/n/10 circlize::circos.par()\T1/ptm/m/n/10 ,
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\T1/zi4/m/n/10 circlize::circos.genomicDensity() \T1/ptm/m/n/10 and \T1/zi4/m/n
/10 circlize::circos.genomicLabels()
[11]
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[]\T1/ptm/m/n/10 Other Plot-ting func-tions: [][]\T1/zi4/m/n/10 CIS_volcano_plo
t[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 HSC_population_plot[][][]()\T1/ptm
/m/n/10 , [][]\T1/zi4/m/n/10 integration_alluvial_plot[][][]()\T1/ptm/m/n/10 ,
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\T1/zi4/m/n/10 ashpublications . org / blood / article / 117 / 20 / 5332 / 2120
6 / Lentiviral-[]vector-[]common-[]integration-[]sites-[]in$[][]
[12]
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[]\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 comparison_mat
rix[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm
/m/n/10 , [][]\T1/zi4/m/n/10 cumulative_count_union[][][]()\T1/ptm/m/n/10 ,
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[15]
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[]\T1/ptm/m/n/10 Other Plot-ting func-tions: [][]\T1/zi4/m/n/10 HSC_population_
plot[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 circos_genomic_density[][][]()\
T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 integration_alluvial_plot[][][]()\T1/ptm/m/n
/10 ,
[16]
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[]\T1/ptm/m/n/10 A named list of in-te-gra-tion ma-tri-ces, ide-ally ob-tained
via [][]im-port_parallel_Vispa2Matrices_interactive[][][]
[17]
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[]\T1/ptm/m/n/10 An in-te-gra-tion ma-trix - aka a data frame that in-cludes th
e \T1/zi4/m/n/10 mandatory_IS_vars()
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\T1/ptm/m/n/10 as columns. The ma-trix can ei-ther be ag-gre-gated (via \T1/zi4
/m/n/10 aggregate_values_by_key()\T1/ptm/m/n/10 )
[18] [19]
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\T1/ptm/m/n/10 data frame con-tains the ref-er-ence of pre-recalibration val-ue
s for \T1/zi4/m/n/10 chr\T1/ptm/m/n/10 , \T1/zi4/m/n/10 strand \T1/ptm/m/n/10 a
nd \T1/zi4/m/n/10 integration_locus
[20] [21]
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[]\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 CIS_grubbs[][]
[]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 comparison_matrix[][][]()\T1/ptm/m/n/10
, [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n
/10 cumulative_is[][][]()\T1/ptm/m/n/10 ,
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[][]\T1/zi4/m/n/10 is_sharing[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 iss_so
urce[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 purity_filter[][][]()\T1/ptm/m/
n/10 , [][]\T1/zi4/m/n/10 sample_statistics[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4
/m/n/10 separate_quant_matrices[][][]()\T1/ptm/m/n/10 ,
[22]
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[]\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 CIS_grubbs[][]
[]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 comparison_matrix[][][]()\T1/ptm/m/n/10
, [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n
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urce[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 purity_filter[][][]()\T1/ptm/m/
n/10 , [][]\T1/zi4/m/n/10 sample_statistics[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4
/m/n/10 separate_quant_matrices[][][]()\T1/ptm/m/n/10 ,
[23]
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[]\T1/ptm/m/it/10 Possible choices for the \T1/zi4/m/n/10 dates_format \T1/ptm/
m/it/10 pa-
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/10 ,
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[24] [25] [26] [27]
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[]\T1/ptm/m/n/10 Other Util-ity func-tions: [][]\T1/zi4/m/n/10 as_sparse_matrix
[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 generate_Vispa2_launch_AF[][][]()\T
1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 unzip_file_system[][][]()
[28]
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[]\T1/ptm/m/n/10 You cor-reclty type names in cor-re-spond-ing po-si-tions, for
ex-am-ple c("CLOEXP", "PROJECT1100",
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[]\T1/ptm/m/n/10 Other Util-ity func-tions: [][]\T1/zi4/m/n/10 as_sparse_matrix
[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 generate_blank_association_file[][]
[]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 unzip_file_system[][][]()
[29]
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[]\T1/ptm/m/n/10 Other Plot-ting func-tions: [][]\T1/zi4/m/n/10 CIS_volcano_plo
t[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 circos_genomic_density[][][]()\T1/
ptm/m/n/10 , [][]\T1/zi4/m/n/10 integration_alluvial_plot[][][]()\T1/ptm/m/n/10
,
[30] [31]
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[]\T1/ptm/m/n/10 The cell types to in-clude in the mod-els. Note that the match
-ing is case-insensitive.
Overfull \hbox (2.29784pt too wide) in paragraph at lines 1822--1831
\T1/ptm/m/n/10 orig-i-nal ma-trix are kept if the se-quence count value is grea
ter or equal than the \T1/zi4/m/n/10 seqCount_threshold
[32] [33]
Overfull \hbox (5.10971pt too wide) in paragraph at lines 1909--1912
\T1/ptm/m/n/10 no re-port should be pro-duced. De-faults to \T1/zi4/m/n/10 {use
r_home}/ISAnalytics_reports\T1/ptm/m/n/10 .
Overfull \hbox (115.40988pt too wide) in paragraph at lines 1933--1937
[]\T1/ptm/m/n/10 Other Im-port func-tions: [][]\T1/zi4/m/n/10 import_Vispa2_sta
ts[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 import_parallel_Vispa2Matrices[][
][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 import_single_Vispa2Matrix[][][]()
[34]
Overfull \hbox (5.10971pt too wide) in paragraph at lines 1996--1999
\T1/ptm/m/n/10 no re-port should be pro-duced. De-faults to \T1/zi4/m/n/10 {use
r_home}/ISAnalytics_reports\T1/ptm/m/n/10 .
Overfull \hbox (25.32918pt too wide) in paragraph at lines 2012--2014
[]\T1/ptm/m/n/10 <[][]\T1/zi4/m/n/10 dynamic-dots[][][]\T1/ptm/m/n/10 > Ad-di-t
ional named ar-gu-ments to pass to \T1/zi4/m/n/10 ìmport_association_file
Overfull \hbox (80.40988pt too wide) in paragraph at lines 2023--2027
[]\T1/ptm/m/n/10 Other Im-port func-tions: [][]\T1/zi4/m/n/10 import_Vispa2_sta
ts[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 import_association_file[][][]()\T
1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 import_single_Vispa2Matrix[][][]()
[35]
Overfull \hbox (64.31819pt too wide) in paragraph at lines 2085--2087
[]\T1/ptm/m/n/10 For more de-tails see the "How to use im-port func-tions" vi-g
nette: \T1/zi4/m/n/10 vignette("import_functions_howto",package
[36]
Overfull \hbox (100.40988pt too wide) in paragraph at lines 2094--2098
[]\T1/ptm/m/n/10 Other Im-port func-tions: [][]\T1/zi4/m/n/10 import_Vispa2_sta
ts[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 import_association_file[][][]()\T
1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 import_parallel_Vispa2Matrices[][][]()
Overfull \hbox (3.81735pt too wide) in paragraph at lines 2143--2146
\T1/ptm/m/n/10 el-e-ments rep-re-sent reg-u-lar ex-pres-sions. For de-faults se
e [][]de-fault_iss_file_prefixes[][][].
[37]
Overfull \hbox (5.10971pt too wide) in paragraph at lines 2155--2158
\T1/ptm/m/n/10 no re-port should be pro-duced. De-faults to \T1/zi4/m/n/10 {use
r_home}/ISAnalytics_reports\T1/ptm/m/n/10 .
[38] [39]
Overfull \hbox (32.36969pt too wide) in paragraph at lines 2274--2281
[]\T1/ptm/m/n/10 Other Plot-ting func-tions: [][]\T1/zi4/m/n/10 CIS_volcano_plo
t[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 HSC_population_plot[][][]()\T1/ptm
/m/n/10 , [][]\T1/zi4/m/n/10 circos_genomic_density[][][]()\T1/ptm/m/n/10 ,
[40]
Overfull \hbox (95.20969pt too wide) in paragraph at lines 2396--2408
[]\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 CIS_grubbs[][]
[]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 comparison_matrix[][][]()\T1/ptm/m/n/10
, [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n
/10 cumulative_count_union[][][]()\T1/ptm/m/n/10 ,
Overfull \hbox (55.36096pt too wide) in paragraph at lines 2396--2408
[][]\T1/zi4/m/n/10 cumulative_is[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 is_
sharing[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 purity_filter[][][]()\T1/ptm
/m/n/10 , [][]\T1/zi4/m/n/10 sample_statistics[][][]()\T1/ptm/m/n/10 , [][]\T1/
zi4/m/n/10 separate_quant_matrices[][][]()\T1/ptm/m/n/10 ,
[41] [42]
Overfull \hbox (122.32698pt too wide) in paragraph at lines 2500--2505
[]\T1/ptm/m/n/10 The func-tion ac-cepts mul-ti-ple in-puts for dif-fer-ent sce-
nar-ios, please re-fer to the vi-gnette \T1/zi4/m/n/10 vignette("sharing_analys
es",package
[43]
Overfull \hbox (95.20969pt too wide) in paragraph at lines 2528--2540
[]\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 CIS_grubbs[][]
[]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 comparison_matrix[][][]()\T1/ptm/m/n/10
, [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n
/10 cumulative_count_union[][][]()\T1/ptm/m/n/10 ,
Overfull \hbox (55.36096pt too wide) in paragraph at lines 2528--2540
[][]\T1/zi4/m/n/10 cumulative_is[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 iss
_source[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 purity_filter[][][]()\T1/ptm
/m/n/10 , [][]\T1/zi4/m/n/10 sample_statistics[][][]()\T1/ptm/m/n/10 , [][]\T1/
zi4/m/n/10 separate_quant_matrices[][][]()\T1/ptm/m/n/10 ,
[44]
Overfull \hbox (51.20859pt too wide) in paragraph at lines 2611--2613
[]\T1/ptm/m/n/10 These are all the pos-si-ble val-ues for the \T1/zi4/m/n/10 ma
tching_opt \T1/ptm/m/n/10 pa-ram-e-ter in \T1/zi4/m/n/10 import_parallel_vispa2
Matrices_auto\T1/ptm/m/n/10 .
[45] [46]
Overfull \hbox (5.10971pt too wide) in paragraph at lines 2716--2719
\T1/ptm/m/n/10 no re-port should be pro-duced. De-faults to \T1/zi4/m/n/10 {use
r_home}/ISAnalytics_reports\T1/ptm/m/n/10 .
[47] [48] [49] [50]
Overfull \hbox (95.20969pt too wide) in paragraph at lines 2973--2985
[]\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 CIS_grubbs[][]
[]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 comparison_matrix[][][]()\T1/ptm/m/n/10
, [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n
/10 cumulative_count_union[][][]()\T1/ptm/m/n/10 ,
Overfull \hbox (40.36096pt too wide) in paragraph at lines 2973--2985
[][]\T1/zi4/m/n/10 cumulative_is[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 is_
sharing[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 iss_source[][][]()\T1/ptm/m/
n/10 , [][]\T1/zi4/m/n/10 sample_statistics[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4
/m/n/10 separate_quant_matrices[][][]()\T1/ptm/m/n/10 ,
Overfull \hbox (118.70859pt too wide) in paragraph at lines 3008--3012
[]\T1/ptm/m/n/10 These are all the pos-si-ble val-ues for the \T1/zi4/m/n/10 qu
antification_type \T1/ptm/m/n/10 pa-ram-e-ter in \T1/zi4/m/n/10 import_parallel
_vispa2Matrices_interactive
[51]
Overfull \hbox (16.08829pt too wide) in paragraph at lines 3057--3064
\T1/ptm/m/n/10 rea-son you re-moved the col-li-sions by pass-ing only the se-qu
ence count ma-trix to \T1/zi4/m/n/10 remove_collisions()\T1/ptm/m/n/10 ,
Overfull \hbox (25.75836pt too wide) in paragraph at lines 3074--3076
[]\T1/ptm/m/n/10 The se-quence count ma-trix al-ready pro-cessed for col-li-sio
ns via \T1/zi4/m/n/10 remove_collisions()
Overfull \hbox (33.86833pt too wide) in paragraph at lines 3084--3086
[]\T1/ptm/m/n/10 For more de-tails on how to use col-li-sion re-moval func-tion
-al-ity: \T1/zi4/m/n/10 vignette("collision_removal",package
[52] [53] (/usr/share/texlive/texmf-dist/tex/latex/base/t1cmtt.fd)
(/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmtt.fd) [54]
Overfull \hbox (19.7378pt too wide) in paragraph at lines 3226--3236
\T1/ptm/m/n/10 tails re-fer to the vi-gnette "Col-li-sion re-moval func-tion-al
-ity": \T1/zi4/m/n/10 vignette("collision_removal",package
[55]
Overfull \hbox (33.6188pt too wide) in paragraph at lines 3260--3262
[]\T1/ptm/m/n/10 The date col-umn that should be con-sid-ered. Must be one valu
e in \T1/zi4/m/n/10 date_columns_coll()
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\T1/ptm/m/n/10 no re-port should be pro-duced. De-faults to \T1/zi4/m/n/10 {use
r_home}/ISAnalytics_reports\T1/ptm/m/n/10 .
[56]
Overfull \hbox (95.20969pt too wide) in paragraph at lines 3376--3388
[]\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 CIS_grubbs[][]
[]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 comparison_matrix[][][]()\T1/ptm/m/n/10
, [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n
/10 cumulative_count_union[][][]()\T1/ptm/m/n/10 ,
Overfull \hbox (20.36096pt too wide) in paragraph at lines 3376--3388
[][]\T1/zi4/m/n/10 cumulative_is[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 is_
sharing[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 iss_source[][][]()\T1/ptm/m/
n/10 , [][]\T1/zi4/m/n/10 purity_filter[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n
/10 separate_quant_matrices[][][]()\T1/ptm/m/n/10 ,
[57] [58]
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[]\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 CIS_grubbs[][]
[]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 comparison_matrix[][][]()\T1/ptm/m/n/10
, [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n
/10 cumulative_count_union[][][]()\T1/ptm/m/n/10 ,
[59]
Overfull \hbox (32.36969pt too wide) in paragraph at lines 3542--3549
[]\T1/ptm/m/n/10 Other Plot-ting func-tions: [][]\T1/zi4/m/n/10 CIS_volcano_plo
t[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 HSC_population_plot[][][]()\T1/ptm
/m/n/10 , [][]\T1/zi4/m/n/10 circos_genomic_density[][][]()\T1/ptm/m/n/10 ,
[60]
Overfull \hbox (32.36969pt too wide) in paragraph at lines 3617--3624
[]\T1/ptm/m/n/10 Other Plot-ting func-tions: [][]\T1/zi4/m/n/10 CIS_volcano_plo
t[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 HSC_population_plot[][][]()\T1/ptm
/m/n/10 , [][]\T1/zi4/m/n/10 circos_genomic_density[][][]()\T1/ptm/m/n/10 ,
[61]
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\T1/ptm/m/n/10 nu-meric vec-tor for \T1/zi4/m/n/10 threshold \T1/ptm/m/n/10 and
char-ac-ter vec-tors for both \T1/zi4/m/n/10 cols_to_compare \T1/ptm/m/n/10 an
d \T1/zi4/m/n/10 comparators\T1/ptm/m/n/10 .
Overfull \hbox (14.32507pt too wide) in paragraph at lines 3677--3683
\T1/ptm/m/n/10 A fil-ter-ing con-di-tion is ob-tained by com-bin-ing el-e-ment
by el-e-ment \T1/zi4/m/n/10 cols_to_compare \T1/ptm/m/n/10 + \T1/zi4/m/n/10 com
parators
[62] [63]
Overfull \hbox (95.20969pt too wide) in paragraph at lines 3848--3860
[]\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 CIS_grubbs[][]
[]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 comparison_matrix[][][]()\T1/ptm/m/n/10
, [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n
/10 cumulative_count_union[][][]()\T1/ptm/m/n/10 ,
[64] [65]
Overfull \hbox (32.36969pt too wide) in paragraph at lines 3964--3971
[]\T1/ptm/m/n/10 Other Plot-ting func-tions: [][]\T1/zi4/m/n/10 CIS_volcano_plo
t[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 HSC_population_plot[][][]()\T1/ptm
/m/n/10 , [][]\T1/zi4/m/n/10 circos_genomic_density[][][]()\T1/ptm/m/n/10 ,
[66]
Overfull \hbox (12.649pt too wide) in paragraph at lines 4000--4002
[]\T1/zi4/m/n/10 keep = "nothing" \T1/ptm/m/n/10 only keeps the manda-tory colu
mns (\T1/zi4/m/n/10 mandatory_IS_vars()\T1/ptm/m/n/10 ) plus the columns
Overfull \hbox (95.20969pt too wide) in paragraph at lines 4047--4059
[]\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 CIS_grubbs[][]
[]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 comparison_matrix[][][]()\T1/ptm/m/n/10
, [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n
/10 cumulative_count_union[][][]()\T1/ptm/m/n/10 ,
[67]
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[]\T1/ptm/m/n/10 Other Util-ity func-tions: [][]\T1/zi4/m/n/10 as_sparse_matrix
[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 generate_Vispa2_launch_AF[][][]()\T
1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 generate_blank_association_file[][][]()
[68] (/tmp/RtmpR4QPxb/Rbuild13fdf567ab114b/ISAnalytics/.Rd2pdf1310197/Rd2.ind
[69]
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[]| \T1/zi4/m/n/10 clinical_relevant_suspicious_genes\T1/ptm/m/n/10 ,
[70]
Overfull \hbox (23.3567pt too wide) in paragraph at lines 219--222
[]\T1/zi4/m/n/10 import_parallel_Vispa2Matrices_interactive\T1/ptm/m/n/10 ,
LaTeX Font Warning: Font shape `T1/zi4/m/it' undefined
(Font) using `T1/zi4/m/n' instead on input line 302.
[71]) (/tmp/RtmpR4QPxb/Rbuild13fdf567ab114b/ISAnalytics/.Rd2pdf1310197/Rd2.aux)
LaTeX Font Warning: Some font shapes were not available, defaults substituted.
)
(see the transcript file for additional information)pdfTeX warning (dest): name
{Rfn.dynamic.Rdash.dots} has been referenced but does not exist, replaced by a
fixed one
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eplaced by a fixed one
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} has been referenced but does not exist, replaced by a fixed one
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ractive} has been referenced but does not exist, replaced by a fixed one
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f-dist/fonts/enc/dvips/inconsolata/i4-t1-0.enc}</usr/share/texlive/texmf-dist/f
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ts/type1/urw/helvetic/uhvr8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw
/times/utmb8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmr8a.p
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Output written on Rd2.pdf (71 pages, 245283 bytes).
Transcript written on Rd2.log.
Saving output to ‘/tmp/RtmpR4QPxb/Rbuild13fdf567ab114b/ISAnalytics/build/ISAnalytics.pdf’ ...
Done
* creating vignettes ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* looking to see if a ‘data/datalist’ file should be added
* building ‘ISAnalytics_1.4.3.tar.gz’
