Entering edit mode
We would like to run ChIPQC on two samples with narrowPeak files. However, we obtain the error in if (nrow(pv$binding) > 0) { : argument is of length zero, as recorded below. The "runChIPQC.R" script was previously described here: C: ChIPQC without peak calls. Do you know what causes this error, and how it can be resolved?
QCexperiment.csv:
SampleID Tissue Factor bamReads ControlID bamControl Peaks PeakCaller
GATA3_WT tissue GATA3 GATA3.wt.bam GATA3_KO GATA3.ko.bam GATA3_peaks.narrowPeak narrow
SRF_WT tissue SRF SRF.wt.bam SRF_KO SRF.ko.bam SRF_peaks.narrowPeak narrow
In R:
> options(error = recover)
> source("runChIPQC.R", echo=TRUE, max.deparse.length=10000)
> #!/usr/bin/xvfb-run -s "-screen 0 1600x1200x24+32" Rscript
> options(stringsAsFactors=FALSE, bitmapType='cairo')
> library("ChIPQC")
Loading required package: ggplot2
Loading required package: DiffBind
Loading required package: 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 objects are masked from ‘package:stats’:
IQR, mad, xtabs
The following objects are masked from ‘package:base’:
anyDuplicated, append, as.data.frame, cbind, colnames, do.call,
duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect,
is.unsorted, lapply, lengths, Map, mapply, match, mget, order,
paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind,
Reduce, rownames, sapply, setdiff, sort, table, tapply, union,
unique, unsplit
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: ‘S4Vectors’
The following objects are masked from ‘package:base’:
colMeans, colSums, expand.grid, rowMeans, rowSums
Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
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")'.
> samples <- read.csv("QCexperiment.csv", sep="\t", stringsAsFactors=FALSE)
> experiment <- ChIPQC(samples, annotation="mm9")
GATA3_WT tissue GATA3 NA narrow
SRF_WT tissue SRF NA narrow
Error in if (nrow(pv$binding) > 0) { : argument is of length zero
Enter a frame number, or 0 to exit
1: source("runChIPQC.R", echo = TRUE, max.deparse.length = 10000)
2: withVisible(eval(ei, envir))
3: eval(ei, envir)
4: eval(expr, envir, enclos)
5: runChIPQC.R#12: ChIPQC(samples, annotation = "mm9")
6: dba(sampleSheet = experiment, bCorPlot = FALSE, peakCaller = "bed")
7: pv.model(DBA, mask = mask, minOverlap = minOverlap, samplesheet = sampleShe
8: pv.vectors(model, mask = mask, minOverlap = minOverlap, attributes = attrib
Selection: 8
Called from: top level
Browse[1]> pv$binding
CHR START END GATA3_WT SRF_WT
9.000000e+00 3.405637e+07 3.405662e+07 1.043910e-01 5.304492e-02
Browse[1]> nrow(pv$binding)
NULL
> traceback()
8: pv.vectors(model, mask = mask, minOverlap = minOverlap, attributes = attributes,
bAllSame <- (peakcaller == "counts"))
7: pv.model(DBA, mask = mask, minOverlap = minOverlap, samplesheet = sampleSheet,
config = config, caller = peakCaller, format = peakFormat,
scorecol = scoreCol, bLowerBetter = bLowerScoreBetter, skipLines = skipLines,
bAddCallerConsensus = bAddCallerConsensus, bRemoveM = bRemoveM,
bRemoveRandom = bRemoveRandom, filter = filter, attributes = attributes)
6: dba(sampleSheet = experiment, bCorPlot = FALSE, peakCaller = "bed")
5: ChIPQC(samples, annotation = "mm9") at runChIPQC.R#12
4: eval(expr, envir, enclos)
3: eval(ei, envir)
2: withVisible(eval(ei, envir))
1: source("runChIPQC.R", echo = TRUE, max.deparse.length = 10000)
> sessionInfo()
R version 3.3.0 (2016-05-03)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS release 6.5 (Final)
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] ChIPQC_1.8.2 DiffBind_2.0.2
[3] SummarizedExperiment_1.2.3 Biobase_2.32.0
[5] GenomicRanges_1.24.2 GenomeInfoDb_1.8.1
[7] IRanges_2.6.1 S4Vectors_0.10.1
[9] BiocGenerics_0.18.0 ggplot2_2.1.0
loaded via a namespace (and not attached):
[1] edgeR_3.14.0
[2] splines_3.3.0
[3] TxDb.Hsapiens.UCSC.hg18.knownGene_3.2.2
[4] TxDb.Mmusculus.UCSC.mm10.knownGene_3.2.2
[5] gtools_3.5.0
[6] assertthat_0.1
[7] latticeExtra_0.6-28
[8] amap_0.8-14
[9] RBGL_1.48.1
[10] Rsamtools_1.24.0
[11] Category_2.38.0
[12] RSQLite_1.0.0
[13] backports_1.0.3
[14] lattice_0.20-33
[15] limma_3.28.14
[16] digest_0.6.9
[17] RColorBrewer_1.1-2
[18] XVector_0.12.0
[19] checkmate_1.8.1
[20] colorspace_1.2-6
[21] Matrix_1.2-6
[22] plyr_1.8.4
[23] GSEABase_1.34.0
[24] chipseq_1.22.0
[25] XML_3.98-1.4
[26] pheatmap_1.0.8
[27] ShortRead_1.30.0
[28] biomaRt_2.28.0
[29] genefilter_1.54.2
[30] zlibbioc_1.18.0
[31] xtable_1.8-2
[32] GO.db_3.3.0
[33] scales_0.4.0
[34] brew_1.0-6
[35] gdata_2.17.0
[36] TxDb.Rnorvegicus.UCSC.rn4.ensGene_3.2.2
[37] BiocParallel_1.6.2
[38] tibble_1.1
[39] annotate_1.50.0
[40] GenomicFeatures_1.24.3
[41] survival_2.39-5
[42] magrittr_1.5
[43] systemPipeR_1.6.2
[44] fail_1.3
[45] gplots_3.0.1
[46] hwriter_1.3.2
[47] GOstats_2.38.1
[48] graph_1.50.0
[49] tools_3.3.0
[50] BBmisc_1.9
[51] stringr_1.0.0
[52] sendmailR_1.2-1
[53] munsell_0.4.3
[54] locfit_1.5-9.1
[55] AnnotationDbi_1.34.3
[56] Biostrings_2.40.2
[57] caTools_1.17.1
[58] grid_3.3.0
[59] RCurl_1.95-4.8
[60] TxDb.Celegans.UCSC.ce6.ensGene_3.2.2
[61] rjson_0.2.15
[62] AnnotationForge_1.14.2
[63] bitops_1.0-6
[64] base64enc_0.1-3
[65] gtable_0.2.0
[66] DBI_0.4-1
[67] reshape2_1.4.1
[68] R6_2.1.2
[69] GenomicAlignments_1.8.3
[70] Nozzle.R1_1.1-1
[71] dplyr_0.5.0
[72] rtracklayer_1.32.1
[73] KernSmooth_2.23-15
[74] stringi_1.1.1
[75] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2
[76] BatchJobs_1.6
[77] Rcpp_0.12.5
[78] TxDb.Dmelanogaster.UCSC.dm3.ensGene_3.2.2
[79] TxDb.Mmusculus.UCSC.mm9.knownGene_3.2.2
We are still unable to fix this. We are successfully able to process each sample individually by disabling faceting (as previously mentioned in C: ChIPQC for a single sample (disabling facets)). We are also able to process samples with multiple replicates using the workaround below:
if (!is.null(samples$Replicate) && length(samples$Replicate) > 1) { makeActiveBinding("resultObj", function() experiment, .GlobalEnv) } else { resultObj <- QCsample(experiment)[[1]] }However, we are unable to extend this to the case where we have multiple samples without replicates. Is there a way to apply a similar workaround to our case?
I'll will get back to you when check in and then see if this solves the issue.
thanks,
tom
Ok, great. Thank you, Tom!
Danielle