ELMER 2.7.5
Tiago Chedraoui Silva
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/ELMER |
| Branch: master |
| Last Commit: daf0f59 |
| Last Changed Date: 2019-04-08 13:09:08 -0400 (Mon, 08 Apr 2019) |
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | ERROR | | |
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | ERROR | OK | |
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | ERROR | OK | |
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | [ ERROR ] | skipped | skipped | |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data ELMER
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* checking for file ‘ELMER/DESCRIPTION’ ... OK
* preparing ‘ELMER’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
Loading required package: ELMER.data
Registered S3 methods overwritten by 'ggplot2':
method from
[.quosures rlang
c.quosures rlang
print.quosures rlang
Registered S3 method overwritten by 'R.oo':
method from
throw.default R.methodsS3
Registered S3 method overwritten by 'rvest':
method from
read_xml.response xml2
Attaching package: 'dplyr'
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
Accessing grch37.ensembl.org to get TSS information
Downloading transcripts information from http://grch37.ensembl.org:80/biomart/martservice. Using: Human genes (GRCh37.p13)
Returning distal probes: 15361
Loading required package: SummarizedExperiment
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:dplyr':
combine, intersect, setdiff, union
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, colMeans, colSums, 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, rowMeans,
rowSums, rownames, sapply, setdiff, sort, table, tapply,
union, unique, unsplit, which, which.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following objects are masked from 'package:dplyr':
first, rename
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Attaching package: 'IRanges'
The following objects are masked from 'package:dplyr':
collapse, desc, slice
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")'.
Loading required package: DelayedArray
Loading required package: matrixStats
Attaching package: 'matrixStats'
The following objects are masked from 'package:Biobase':
anyMissing, rowMedians
The following object is masked from 'package:dplyr':
count
Loading required package: BiocParallel
Attaching package: 'DelayedArray'
The following objects are masked from 'package:matrixStats':
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following objects are masked from 'package:base':
aperm, apply, rowsum
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Creating a SummarizedExperiment from gene expression input
Accessing grch37.ensembl.org to get gene information
Downloading genome information (try:0) Using: Human genes (GRCh37.p13)
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Creating a SummarizedExperiment from DNA methylation input
Checking if samples have both DNA methylation and Gene expression and if they are in the same order...
Starting to add information to samples
=> Add clinical information to samples
Add FFPE information. More information at:
=> https://cancergenome.nih.gov/cancersselected/biospeccriteria
=> http://gdac.broadinstitute.org/runs/sampleReports/latest/FPPP_FFPE_Cases.html
=> Adding subtype information to samples
lusc subtype information from:doi:10.1038/nature11404
Creating MultiAssayExperiment
MAE saved as: mae.rda
ELMER will search for probes hypomethylated in group Primary solid Tumor (n:226) compared to Solid Tissue Normal (n:8)
ooo Arguments ooo
o Number of probes: 1622
o Beta value difference cut-off: 0.3
o FDR cut-off: 0.01
o Mode: unsupervised
o % of samples per group in each comparison: 0.2
o Min number of samples per group in each comparison: 5
o Nb of samples group1 in each comparison: 45
o Nb of samples group2 in each comparison: 5
Output direction: result
ooooooooooooooooo
Saving results
Number of relevant probes found: 704
Parsed with column specification:
cols(
probe = col_character(),
pvalue = col_double(),
Primary.solid.Tumor_Minus_Solid.Tissue.Normal = col_double(),
adjust.p = col_double()
)
Searching for the 20 near genes
Identifying gene position for each probe
Selecting U (unmethylated) and M (methylated) groups. Each groups has 20% of samples
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* Filtering probes
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For more information see function preAssociationProbeFiltering
Making sure we have at least 5% of beta values lesser than 0.3 and 5% of beta values greater 0.3.
Removing 585 probes out of 1622
Calculating Pp (probe - gene) for all nearby genes
File created: result/getPair.hypo.all.pairs.statistic.csv
Calculating Pr (random probe - gene). Permutating 100 probes for 746 genes
Calculate empirical P value.
Loading object: Probes.motif.hg19.450K
Retrieving TFClass family classification from ELMER.data.
Retrieving TFClass subfamily classification from ELMER.data.
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** Filtering motifs based on quality
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Number of enriched motifs with quality:
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=> A: 5
=> B: 1
=> C: 1
=> D: 4
=> S: 0
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Considering only motifs with quality from A up to DS: 11 motifs are enriched.
Selecting U (unmethylated) and M (methylated) groups. Each groups has 20% of samples
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** Downloading TF list from Lambert, Samuel A., et al. The human transcription factors. Cell 172.4 (2018): 650-665.
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Accessing TF families from TFClass database to indentify known potential TF
Retrieving TFClass family classification from ELMER.data.
Retrieving TFClass subfamily classification from ELMER.data.
Calculating the average methylation at all motif-adjacent probes
Performing Mann-Whitney U test
Finding potential TF and known potential TF
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Creating a SummarizedExperiment from gene expression input
Accessing grch37.ensembl.org to get gene information
Downloading genome information (try:0) Using: Human genes (GRCh37.p13)
Loading from disk
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
Creating a SummarizedExperiment from DNA methylation input
Checking if samples have both DNA methylation and Gene expression and if they are in the same order...
Starting to add information to samples
=> Add clinical information to samples
Add FFPE information. More information at:
=> https://cancergenome.nih.gov/cancersselected/biospeccriteria
=> http://gdac.broadinstitute.org/runs/sampleReports/latest/FPPP_FFPE_Cases.html
=> Adding subtype information to samples
lusc subtype information from:doi:10.1038/nature11404
Creating MultiAssayExperiment
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
Creating a SummarizedExperiment from gene expression input
Accessing grch37.ensembl.org to get gene information
Downloading genome information (try:0) Using: Human genes (GRCh37.p13)
Loading from disk
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
Creating a SummarizedExperiment from DNA methylation input
Removing samples not found in both DNA methylation and gene expression (we are considering the names of the gene expression and DNA methylation columns to be the same)
MAE saved as: mae_hg19_450K.rda
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Creating a SummarizedExperiment from gene expression input
Accessing www.ensembl.org to get gene information
Downloading genome information (try:0) Using:
Quitting from lines 130-185 (input.Rmd)
Error: processing vignette 'input.Rmd' failed with diagnostics:
$ operator is invalid for atomic vectors
Execution halted