Entering edit mode
Hi,
I have peak file for four different condition without replicate. I converted the text file to Bed file by taking column 2,3,4,8 and 5 which is chr, start, end, score and strand respectively and also removed first 40 line having "#' in the begining. and then created samplesheet "sample.csv" having column Id, tissue, condition, bamreads, bamconrtol, peak, peakcaller.
steps I followed
library(DiffBind)
sample=read.csv("sample.csv")
COR =dba(sampleSheet="sample.csv")
## When i am running below command I am getting error "Error in pv$peaks[[i]] : subscript out of bounds"
COR = dba.count(COR, minOverlap=3)
1.What is this error?
2.Why I am getting this error ?
3.What is the solution of this?
Thanks in advance.
Gyan Prakash Mishra
1.) What is the output from
traceback(), run right after you get that error?2.) What is the output for
sessionInfo()after you have loaded DiffBind?Hi James,
Here are the ouputs.
output of sessionInfo()
> sessionInfo()
R Under development (unstable) (2015-07-11 r68646)
Platform: x86_64-unknown-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats4 parallel stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] DiffBind_1.14.5 RSQLite_1.0.0 DBI_0.3.1
[4] locfit_1.5-9.1 GenomicAlignments_1.4.1 Rsamtools_1.20.4
[7] Biostrings_2.36.1 XVector_0.8.0 limma_3.24.14
[10] GenomicRanges_1.20.5 GenomeInfoDb_1.4.1 IRanges_2.2.5
[13] S4Vectors_0.6.3 BiocGenerics_0.14.0
loaded via a namespace (and not attached):
[1] Rcpp_0.12.0 lattice_0.20-33 GO.db_3.1.2
[4] gtools_3.5.0 digest_0.6.8 plyr_1.8.3
[7] futile.options_1.0.0 BatchJobs_1.6 ShortRead_1.26.0
[10] ggplot2_1.0.1 gplots_2.17.0 zlibbioc_1.14.0
[13] annotate_1.46.1 gdata_2.17.0 Matrix_1.2-2
[16] checkmate_1.6.2 systemPipeR_1.2.16 proto_0.3-10
[19] GOstats_2.34.0 splines_3.3.0 BiocParallel_1.2.9
[22] stringr_1.0.0 pheatmap_1.0.7 munsell_0.4.2
[25] sendmailR_1.2-1 base64enc_0.1-3 BBmisc_1.9
[28] fail_1.2 edgeR_3.10.2 XML_3.98-1.3
[31] AnnotationForge_1.10.1 MASS_7.3-43 bitops_1.0-6
[34] grid_3.3.0 RBGL_1.44.0 xtable_1.7-4
[37] GSEABase_1.30.2 gtable_0.1.2 magrittr_1.5
[40] scales_0.2.5 graph_1.46.0 KernSmooth_2.23-15
[43] amap_0.8-14 stringi_0.5-5 hwriter_1.3.2
[46] reshape2_1.4.1 genefilter_1.50.0 latticeExtra_0.6-26
[49] futile.logger_1.4.1 brew_1.0-6 rjson_0.2.15
[52] lambda.r_1.1.7 RColorBrewer_1.1-2 tools_3.3.0
[55] Biobase_2.28.0 Category_2.34.2 survival_2.38-3
[58] AnnotationDbi_1.30.1 colorspace_1.2-6 caTools_1.17.1
output of traceback()
> traceback()
4: pv.listadd(peaks, pv$peaks[[i]])
3: pv.vectors(pv, (numpeaks - numAdded + 1):numpeaks, minOverlap = 1,
bAnalysis = F, bAllSame = T)
2: pv.counts(DBA, peaks = peaks, minOverlap = minOverlap, defaultScore = score,
bLog = bLog, insertLength = fragmentSize, bOnlyCounts = T,
bCalledMasks = TRUE, minMaxval = filter, bParallel = bParallel,
bUseLast = bUseLast, bWithoutDupes = bRemoveDuplicates, bScaleControl = bScaleControl,
filterFun = filterFun, bLowMem = bUseSummarizeOverlaps, readFormat = readFormat,
summits = summits, minMappingQuality = mapQCth)
1: dba.count(NCOR1, minOverlap = 3)