Entering edit mode
Hello,
I have successfully run derfinder following the tutorial on some human data, but now I am getting an error when trying to go through the same process with some mouse data. Any help would be appreciated.
Thanks,
Paul Schaughency
Here is the relevant log:
> source("http://bioconductor.org/biocLite.R")
Bioconductor version 3.0 (BiocInstaller 1.16.4), ?biocLite for help
A new version of Bioconductor is available after installing the most recent version of R; see http://bioconductor.org/install
>
> library('derfinder')
> library('GenomicRanges')
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 object is masked from ‘package:stats’:
xtabs
The following objects are masked from ‘package:base’:
anyDuplicated, append, as.data.frame, as.vector, cbind, colnames, do.call, duplicated, eval, evalq, Filter, Find, get, intersect, is.unsorted, lapply, Map, mapply,
match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rep.int, rownames, sapply, setdiff, sort, table, tapply, union, unique,
unlist, unsplit
Loading required package: S4Vectors
Loading required package: stats4
Loading required package: IRanges
Loading required package: GenomeInfoDb
> filenames <- c('GFP_plus_k_sorted.bam' ,'GFP_minus_k_sorted.bam')
> pheno <- data.frame(sample=filenames, group=c('GFP_plus', 'GFP_minus'))
>
> options(species = 'mus_musculus')
> fullCov <- fullCoverage(filenames, chrs=c('chr1'))
2015-06-05 13:54:16 fullCoverage: processing chromosome chr1
2015-06-05 13:54:16 loadCoverage: finding chromosome lengths
2015-06-05 13:54:16 loadCoverage: loading BAM file GFP_plus_k_sorted.bam
2015-06-05 13:54:38 loadCoverage: loading BAM file GFP_minus_k_sorted.bam
2015-06-05 13:54:55 loadCoverage: applying the cutoff to the merged data
2015-06-05 13:54:55 filterData: originally there were 195471971 rows, now there are 195471971 rows. Meaning that 0 percent was filtered.
> filteredCov <- lapply(fullCov, filterData, cutoff = 2)
2015-06-05 13:55:08 filterData: originally there were 195471971 rows, now there are 43712465 rows. Meaning that 77.64 percent was filtered.
> sampleDepths <- sampleDepth(collapseFullCoverage(fullCov), 1)
2015-06-05 13:55:10 sampleDepth: Calculating sample quantiles
2015-06-05 13:55:10 sampleDepth: Calculating sample adjustments
> models <- makeModels(sampleDepths, testvars = pheno$group)
Warning messages:
1: In makeModels(sampleDepths, testvars = pheno$group) :
Dropping from the alternative model matrix (mod) the column(s) sampleDepths as the matrix is not full rank.
2: In makeModels(sampleDepths, testvars = pheno$group) :
Dropping from the null model matrix (mod0) the column(s) sampleDepths as they were dropped in the alternative model matrix (mod).
> dir.create('analysisResultsgfp')
Warning message:
In dir.create("analysisResultsgfp") : 'analysisResultsgfp' already exists
> originalWd <- getwd()
> setwd(file.path(originalWd, 'analysisResultsgfp'))
> system.time(resultschr1 <- analyzeChr( chr= 'chr1', filteredCov$chr1, models, groupInfo = pheno$group, runAnnotation = FALSE, writeOutput = TRUE, cutoffFstat = 5e-02, nPermute = 20, seeds = 20140923 + seq_len(20), returnOutput = TRUE))
2015-06-05 13:55:25 analyzeChr: Pre-processing the coverage data
2015-06-05 13:56:23 analyzeChr: Calculating statistics
2015-06-05 13:56:23 calculateStats: calculating the F-statistics
2015-06-05 13:56:33 analyzeChr: Calculating pvalues
2015-06-05 13:56:33 analyzeChr: Using the following theoretical cutoff for the F-statistics NaN
2015-06-05 13:56:33 calculatePvalues: identifying data segments
2015-06-05 13:56:33 findRegions: segmenting F-stats information
Error in .local(x, lower, upper, ...) : 'lower' must be a single number
In addition: Warning message:
In qf(cutoffFstat, df1 - df0, n - df1, lower.tail = FALSE) : NaNs produced
Timing stopped at: 64.51 4.25 68.065
> ## Session information
> options(width = 90)
> devtools::session_info()
Session info -----------------------------------------------------------------------------
setting value
version R version 3.1.3 (2015-03-09)
system x86_64, darwin14.1.0
ui RStudio (0.98.1091)
language (EN)
collate en_US.UTF-8
tz America/New_York
Packages ---------------------------------------------------------------------------------
package * version date source
acepack 1.3-3.3 2014-11-24 CRAN (R 3.1.3)
AnnotationDbi 1.28.2 2015-03-20 Bioconductor
base64enc 0.1-2 2014-06-26 CRAN (R 3.1.3)
BatchJobs 1.6 2015-03-18 CRAN (R 3.1.3)
BBmisc 1.9 2015-02-03 CRAN (R 3.1.3)
Biobase 2.26.0 2015-03-18 Bioconductor
BiocGenerics * 0.12.1 2015-03-18 Bioconductor
BiocInstaller * 1.16.4 2015-05-14 Bioconductor
BiocParallel 1.0.3 2015-03-18 Bioconductor
biomaRt 2.22.0 2015-03-18 Bioconductor
Biostrings 2.34.1 2015-03-18 Bioconductor
bitops 1.0-6 2013-08-17 CRAN (R 3.1.3)
brew 1.0-6 2011-04-13 CRAN (R 3.1.3)
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cluster 2.0.1 2015-01-31 CRAN (R 3.1.3)
codetools 0.2-11 2015-03-10 CRAN (R 3.1.3)
colorspace 1.2-6 2015-03-11 CRAN (R 3.1.3)
DBI 0.3.1 2014-09-24 CRAN (R 3.1.3)
derfinder * 1.0.10 2015-05-15 Bioconductor
derfinderHelper 1.0.4 2015-03-18 Bioconductor
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