Fangda Song
| Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022) |
| git_url: https://git.bioconductor.org/packages/BUSseq |
| git_branch: RELEASE_3_14 |
| git_last_commit: aae9920 |
| git_last_commit_date: 2021-10-26 13:10:51 -0400 (Tue, 26 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.14 |
|
This page was generated on 2022-04-13 12:06:16 -0400 (Wed, 13 Apr 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4324 |
| tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4077 |
| machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4137 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
|
To the developers/maintainers of the BUSseq package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to [email protected]:packages/BUSseq.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 232/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BUSseq 1.0.0 (landing page) Fangda Song
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: BUSseq |
| Version: 1.0.0 |
| Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BUSseq.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings BUSseq_1.0.0.tar.gz |
| StartedAt: 2022-04-12 16:43:16 -0400 (Tue, 12 Apr 2022) |
| EndedAt: 2022-04-12 16:54:08 -0400 (Tue, 12 Apr 2022) |
| EllapsedTime: 651.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BUSseq.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BUSseq.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings BUSseq_1.0.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/BUSseq.Rcheck' * using R version 4.1.3 (2022-03-10) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'BUSseq/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'BUSseq' version '1.0.0' * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking whether package 'BUSseq' can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking 'build' directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * loading checks for arch 'i386' ** checking whether the package can be loaded ... OK ** checking whether the package can be loaded with stated dependencies ... OK ** checking whether the package can be unloaded cleanly ... OK ** checking whether the namespace can be loaded with stated dependencies ... OK ** checking whether the namespace can be unloaded cleanly ... OK * loading checks for arch 'x64' ** checking whether the package can be loaded ... OK ** checking whether the package can be loaded with stated dependencies ... OK ** checking whether the package can be unloaded cleanly ... OK ** checking whether the namespace can be loaded with stated dependencies ... OK ** checking whether the namespace can be unloaded cleanly ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of 'data' directory ... OK * checking data for non-ASCII characters ... OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... OK * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking compiled code ... NOTE Note: information on .o files for i386 is not available Note: information on .o files for x64 is not available File 'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BUSseq/libs/i386/BUSseq.dll': Found '_exit', possibly from '_exit' (C) Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Found 'exit', possibly from 'exit' (C), 'stop' (Fortran) Found 'printf', possibly from 'printf' (C) File 'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BUSseq/libs/x64/BUSseq.dll': Found '_exit', possibly from '_exit' (C) Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Found 'exit', possibly from 'exit' (C), 'stop' (Fortran) Found 'printf', possibly from 'printf' (C) Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs. The detected symbols are linked into the code but might come from libraries and not actually be called. See 'Writing portable packages' in the 'Writing R Extensions' manual. * checking files in 'vignettes' ... OK * checking examples ... ** running examples for arch 'i386' ... OK ** running examples for arch 'x64' ... OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... ** running tests for arch 'i386' ... Running 'BUSseq_example.R' OK ** running tests for arch 'x64' ... Running 'BUSseq_example.R' OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in 'inst/doc' ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 NOTE See 'C:/Users/biocbuild/bbs-3.14-bioc/meat/BUSseq.Rcheck/00check.log' for details.
BUSseq.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/BUSseq_1.0.0.tar.gz && rm -rf BUSseq.buildbin-libdir && mkdir BUSseq.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BUSseq.buildbin-libdir BUSseq_1.0.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL BUSseq_1.0.0.zip && rm BUSseq_1.0.0.tar.gz BUSseq_1.0.0.zip
###
##############################################################################
##############################################################################
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 334k 100 334k 0 0 352k 0 --:--:-- --:--:-- --:--:-- 352k
100 334k 100 334k 0 0 352k 0 --:--:-- --:--:-- --:--:-- 352k
install for i386
* installing *source* package 'BUSseq' ...
** using staged installation
** libs
C:/Users/BIOCBU~1/BBS-3~1.14-/R/share/make/winshlib.mk:16: warning: overriding recipe for target 'BUSseq.dll'
Makevars.win:9: warning: ignoring old recipe for target 'BUSseq.dll'
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c BUSseq.cpp -o BUSseq.o
BUSseq.cpp: In function 'double postprob_DE_thr_fun(double*, double, int, int)':
BUSseq.cpp:964:69: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
while((fdr <= _fdr_threshold) & (kappa <= postprob_DE_thr) & (i < (unsigned)vec_PPI.size())){
~~^~~~~~~~~~~~~~~~~~~~~~~~~~
BUSseq.cpp: In function 'void BUSseq_inference(int*, int*, int*, int*, char**, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, int*, double*, int*, double*)':
BUSseq.cpp:2674:7: warning: variable 'All_Drop' set but not used [-Wunused-but-set-variable]
bool All_Drop = true;
^~~~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c rngstream.cpp -o rngstream.o
C:/rtools40/mingw32/bin/g++ -shared -s -static-libgcc -o BUSseq.dll tmp.def BUSseq.o rngstream.o -fopenmp -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/BUSseq.buildbin-libdir/00LOCK-BUSseq/00new/BUSseq/libs/i386
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'BUSseq'
finding HTML links ... done
BIC_BUSseq html
BUSseq-package html
BUSseq_MCMC html
BUSseqfits_example html
baseline_expression_values html
cell_effect_values html
celltype_effects html
celltype_mean_expression html
celltypes html
corrected_read_counts html
dropout_coefficient_values html
heatmap_data_BUSseq html
imputed_read_counts html
intrinsic_genes_BUSseq html
location_batch_effects html
overdispersions html
raw_read_counts html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'BUSseq' ...
** libs
C:/Users/BIOCBU~1/BBS-3~1.14-/R/share/make/winshlib.mk:16: warning: overriding recipe for target 'BUSseq.dll'
Makevars.win:9: warning: ignoring old recipe for target 'BUSseq.dll'
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c BUSseq.cpp -o BUSseq.o
BUSseq.cpp: In function 'double postprob_DE_thr_fun(double*, double, int, int)':
BUSseq.cpp:964:69: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
while((fdr <= _fdr_threshold) & (kappa <= postprob_DE_thr) & (i < (unsigned)vec_PPI.size())){
~~^~~~~~~~~~~~~~~~~~~~~~~~~~
BUSseq.cpp: In function 'void BUSseq_inference(int*, int*, int*, int*, char**, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, int*, double*, int*, double*)':
BUSseq.cpp:2674:7: warning: variable 'All_Drop' set but not used [-Wunused-but-set-variable]
bool All_Drop = true;
^~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c rngstream.cpp -o rngstream.o
C:/rtools40/mingw64/bin/g++ -shared -s -static-libgcc -o BUSseq.dll tmp.def BUSseq.o rngstream.o -fopenmp -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/BUSseq.buildbin-libdir/BUSseq/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'BUSseq' as BUSseq_1.0.0.zip
* DONE (BUSseq)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'BUSseq' successfully unpacked and MD5 sums checked
|
BUSseq.Rcheck/tests_i386/BUSseq_example.Rout
R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> #######################################
> # Apply BUSseq to the Simulation Data #
> #######################################
> library(BUSseq)
> library(SingleCellExperiment)
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats
Attaching package: 'MatrixGenerics'
The following objects are masked from 'package:matrixStats':
colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
colWeightedMeans, colWeightedMedians, colWeightedSds,
colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
rowWeightedSds, rowWeightedVars
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: IRanges
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: 'Biobase'
The following object is masked from 'package:MatrixGenerics':
rowMedians
The following objects are masked from 'package:matrixStats':
anyMissing, rowMedians
> RawCountData <- assay(BUSseqfits_example, "counts")
> batch_ind <- unlist(colData(BUSseqfits_example))
> sce <- SingleCellExperiment(assays = list(counts = RawCountData),
+ colData = DataFrame(Batch_ind = batch_ind))
> BUSseqfits_res <- BUSseq_MCMC(ObservedData = sce,
+ seed = 1234, n.cores = 2,
+ n.celltypes = 4, n.iterations = 500)
conducting the posterior sampling...
[> ] Finish 0.00k/0.50k iterations.
[====> ] Finish 0.05k/0.50k iterations.
[========> ] Finish 0.10k/0.50k iterations.
[============> ] Finish 0.15k/0.50k iterations.
[================> ] Finish 0.20k/0.50k iterations.
[====================> ] Finish 0.25k/0.50k iterations.
[========================> ] Finish 0.30k/0.50k iterations.
[============================> ] Finish 0.35k/0.50k iterations.
[================================> ] Finish 0.40k/0.50k iterations.
[====================================> ] Finish 0.45k/0.50k iterations.
[========================================] Finish 0.50k/0.50k iterations.
The MCMC sampling takes: 1.762 mins
conducting the posterior inference...
Posterior inference takes: 1.84 mins
>
> ################################################
> # Extract Estimates from the BUSseqfits Object #
> ################################################
>
> #return cell type indicators
> w.est <- celltypes(BUSseqfits_res)
Batch 1 cells' cell type indicators: 1,1,1... ...
Batch 2 cells' cell type indicators: 1,1,1... ...
The output format is an N-dimensional verctor.
>
> #return the intercept and odds ratio of the logistic regression
> #for dropout events
> gamma.est <- dropout_coefficient_values(BUSseqfits_res)
The output format is a matrix.
Each row represents a batch, the first column corresponds to intercept and the second column is the odd ratio.
>
> #return the log-scale baseline expression values
> alpha.est <- baseline_expression_values(BUSseqfits_res)
The output format is a vector.
>
> #return the cell-type effects
> beta.est <- celltype_effects(BUSseqfits_res)
The output format is a matrix.
Each row represents a gene, and each column corresponds to a cell type.
>
> #return the mean expression levels
> mu.est <- celltype_mean_expression(BUSseqfits_res)
The output format is a matrix.
Each row represents a gene, and each column corresponds to a cell type.
>
> #return the cell-specific global effects
> delta.est <- cell_effect_values(BUSseqfits_res)
The output format is an N-dimensional vector.
>
> #return the location batch effects
> nu.est <- location_batch_effects(BUSseqfits_res)
The output format is a matrix.
Each row represents a gene, and each column corresponds to a batch.
>
> #return the overdispersion parameters
> phi.est <- overdispersions(BUSseqfits_res)
The output format is a matrix.
Each row represents a gene, and each column corresponds to a batch.
>
> #return the intrinsic gene indices
> D.est <- intrinsic_genes_BUSseq(BUSseqfits_res)
>
> #return the BIC value
> BIC <- BIC_BUSseq(BUSseqfits_res)
BIC is 460947.370514477
The output is a scalar.
>
> #return the raw read count matrix
> CountData_raw <- raw_read_counts(BUSseqfits_res)
The output format is a matrix, in which each row represents a gene and each column does a cell.
>
> #return the imputed read count matrix
> CountData_imputed <- imputed_read_counts(BUSseqfits_res)
The output format is a matrix, in which each row represents a gene and each column does a cell.
>
> #return the corrected read count matrix
> BUSseqfits_res <- corrected_read_counts(BUSseqfits_res)
correcting read counts...
The corrected read count matrix is added into the output "SingleCellExperiment" object.
>
> #################
> # Visualization #
> #################
> #generate the heatmap of raw read count data
> heatmap_data_BUSseq(BUSseqfits_res, project_name="Heatmap_raw")
null device
1
>
> #generate the heatmap of imputed read count data
> heatmap_data_BUSseq(BUSseqfits_res, data_type = "Imputed",
+ project_name="Heatmap_imputed")
null device
1
>
> #generate the heatmap of corrected read count data
> heatmap_data_BUSseq(BUSseqfits_res, data_type = "Corrected",
+ project_name="Heatmap_corrected")
null device
1
>
> proc.time()
user system elapsed
245.56 50.70 225.28
|
BUSseq.Rcheck/tests_x64/BUSseq_example.Rout
R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> #######################################
> # Apply BUSseq to the Simulation Data #
> #######################################
> library(BUSseq)
> library(SingleCellExperiment)
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats
Attaching package: 'MatrixGenerics'
The following objects are masked from 'package:matrixStats':
colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
colWeightedMeans, colWeightedMedians, colWeightedSds,
colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
rowWeightedSds, rowWeightedVars
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: IRanges
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: 'Biobase'
The following object is masked from 'package:MatrixGenerics':
rowMedians
The following objects are masked from 'package:matrixStats':
anyMissing, rowMedians
> RawCountData <- assay(BUSseqfits_example, "counts")
> batch_ind <- unlist(colData(BUSseqfits_example))
> sce <- SingleCellExperiment(assays = list(counts = RawCountData),
+ colData = DataFrame(Batch_ind = batch_ind))
> BUSseqfits_res <- BUSseq_MCMC(ObservedData = sce,
+ seed = 1234, n.cores = 2,
+ n.celltypes = 4, n.iterations = 500)
conducting the posterior sampling...
[> ] Finish 0.00k/0.50k iterations.
[====> ] Finish 0.05k/0.50k iterations.
[========> ] Finish 0.10k/0.50k iterations.
[============> ] Finish 0.15k/0.50k iterations.
[================> ] Finish 0.20k/0.50k iterations.
[====================> ] Finish 0.25k/0.50k iterations.
[========================> ] Finish 0.30k/0.50k iterations.
[============================> ] Finish 0.35k/0.50k iterations.
[================================> ] Finish 0.40k/0.50k iterations.
[====================================> ] Finish 0.45k/0.50k iterations.
[========================================] Finish 0.50k/0.50k iterations.
The MCMC sampling takes: 1.677 mins
conducting the posterior inference...
Posterior inference takes: 1.344 mins
>
> ################################################
> # Extract Estimates from the BUSseqfits Object #
> ################################################
>
> #return cell type indicators
> w.est <- celltypes(BUSseqfits_res)
Batch 1 cells' cell type indicators: 1,1,1... ...
Batch 2 cells' cell type indicators: 1,1,1... ...
The output format is an N-dimensional verctor.
>
> #return the intercept and odds ratio of the logistic regression
> #for dropout events
> gamma.est <- dropout_coefficient_values(BUSseqfits_res)
The output format is a matrix.
Each row represents a batch, the first column corresponds to intercept and the second column is the odd ratio.
>
> #return the log-scale baseline expression values
> alpha.est <- baseline_expression_values(BUSseqfits_res)
The output format is a vector.
>
> #return the cell-type effects
> beta.est <- celltype_effects(BUSseqfits_res)
The output format is a matrix.
Each row represents a gene, and each column corresponds to a cell type.
>
> #return the mean expression levels
> mu.est <- celltype_mean_expression(BUSseqfits_res)
The output format is a matrix.
Each row represents a gene, and each column corresponds to a cell type.
>
> #return the cell-specific global effects
> delta.est <- cell_effect_values(BUSseqfits_res)
The output format is an N-dimensional vector.
>
> #return the location batch effects
> nu.est <- location_batch_effects(BUSseqfits_res)
The output format is a matrix.
Each row represents a gene, and each column corresponds to a batch.
>
> #return the overdispersion parameters
> phi.est <- overdispersions(BUSseqfits_res)
The output format is a matrix.
Each row represents a gene, and each column corresponds to a batch.
>
> #return the intrinsic gene indices
> D.est <- intrinsic_genes_BUSseq(BUSseqfits_res)
>
> #return the BIC value
> BIC <- BIC_BUSseq(BUSseqfits_res)
BIC is 460947.370514477
The output is a scalar.
>
> #return the raw read count matrix
> CountData_raw <- raw_read_counts(BUSseqfits_res)
The output format is a matrix, in which each row represents a gene and each column does a cell.
>
> #return the imputed read count matrix
> CountData_imputed <- imputed_read_counts(BUSseqfits_res)
The output format is a matrix, in which each row represents a gene and each column does a cell.
>
> #return the corrected read count matrix
> BUSseqfits_res <- corrected_read_counts(BUSseqfits_res)
correcting read counts...
The corrected read count matrix is added into the output "SingleCellExperiment" object.
>
> #################
> # Visualization #
> #################
> #generate the heatmap of raw read count data
> heatmap_data_BUSseq(BUSseqfits_res, project_name="Heatmap_raw")
null device
1
>
> #generate the heatmap of imputed read count data
> heatmap_data_BUSseq(BUSseqfits_res, data_type = "Imputed",
+ project_name="Heatmap_imputed")
null device
1
>
> #generate the heatmap of corrected read count data
> heatmap_data_BUSseq(BUSseqfits_res, data_type = "Corrected",
+ project_name="Heatmap_corrected")
null device
1
>
> proc.time()
user system elapsed
201.15 47.42 191.15
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BUSseq.Rcheck/examples_i386/BUSseq-Ex.timings
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BUSseq.Rcheck/examples_x64/BUSseq-Ex.timings
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