Entering edit mode
Ryan C. Thompson
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7.9k
@ryan-c-thompson-5618
Last seen 6 weeks ago
Icahn School of Medicine at Mount Sinai…
I am trying to use ChIPQC to analyze my ChIP-seq experiment, and I'm running into a confusing error in the internals of ChIPQC. I have no idea how to work around this error. Can anyone help me debug this? Here is the traceback and sessionInfo.
> cqc <- ChIPQC(
+ experiment = chipqc.exp.df,
+ annotation = "hg19",
+ chromosomes = extractSeqlevels("Homo sapiens", "UCSC") %>%
+ setdiff("chrM"),
+ profileWin = 600)
H3K4me2-Memory-D0-Donor4659 Memory H3K4me2 MemoryD0 D0 1 bed
H3K4me3-Memory-D0-Donor4659 Memory H3K4me3 MemoryD0 D0 1 bed
...
[lines omitted]
...
H3K4me2-Naive-D5-Donor5291 Naive H3K4me2 NaiveD5 D5 4 bed
H3K27me3-Naive-D5-Donor5291 Naive H3K27me3 NaiveD5 D5 4 bed
Compiling annotation...
Using default blacklist for hg19...
Computing metrics for 127 samples...
list
Bam file has 25 contigs
Calculating coverage histogram for chr10
Error in as.factor(unlist(x, use.names = FALSE)) :
error in evaluating the argument 'x' in selecting a method for function 'as.factor': Error in .Call2("Rle_constructor", values, lengths, check, 0L, PACKAGE = "S4Vectors") :
integer overflow while summing elements in 'lengths'
> traceback()
18: as.factor(unlist(x, use.names = FALSE))
17: .Method(...)
16: eval(expr, envir, enclos)
15: eval(.dotsCall, env)
14: eval(.dotsCall, env)
13: standardGeneric("table")
12: table(Cov)
11: is.data.frame(x)
10: colSums(table(Cov))
9: sampleQC(bamFile = reads, bedFile = peaks, GeneAnnotation = annotation,
blklist = blacklist, ChrOfInterest = chromosomes, Window = profileWin,
FragmentLength = fragmentLength, shiftWindowStart = min(shifts),
shiftWindowEnd = max(shifts), runCrossCor = runCrossCor)
8: ChIPQCsample(reads = sample$bam, peaks = sample$peaks, chromosomes = chromosomes,
annotation = annotation, mapQCth = mapQCth, blacklist = blacklist,
profileWin = profileWin, fragmentLength = fragmentLength,
shifts = shifts)
7: FUN(X[[i]], ...)
6: lapply(X, FUN, ...)
5: bplapply(X, FUN, ..., BPREDO = BPREDO, BPPARAM = BPPARAM)
4: bplapply(X, FUN, ..., BPREDO = BPREDO, BPPARAM = BPPARAM)
3: bplapply(samplelist, doChIPQCsample, experiment, chromosomes,
annotation, mapQCth, blacklist, profileWin, fragmentLength,
shifts)
2: bplapply(samplelist, doChIPQCsample, experiment, chromosomes,
annotation, mapQCth, blacklist, profileWin, fragmentLength,
shifts)
1: ChIPQC(experiment = chipqc.exp.df, annotation = "hg19", chromosomes = extractSeqlevels("Homo sapiens",
"UCSC") %>% setdiff("chrM"), profileWin = 600)
> sessionInfo()
R version 3.2.0 (2015-04-16)
Platform: x86_64-unknown-linux-gnu (64-bit)
Running under: Ubuntu 15.04
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] grDevices datasets parallel graphics stats4 stats utils
[8] methods base
other attached packages:
[1] ChIPQC_1.5.3
[2] DiffBind_1.15.3
[3] locfit_1.5-9.1
[4] GenomicAlignments_1.5.17
[5] Rsamtools_1.21.17
[6] limma_3.25.16
[7] mgcv_1.8-7
[8] nlme_3.1-122
[9] BiocParallel_1.3.52
[10] csaw_1.3.13
[11] SummarizedExperiment_0.3.9
[12] doParallel_1.0.8
[13] iterators_1.0.7
[14] org.Hs.eg.db_3.2.1
[15] RSQLite_1.0.0
[16] DBI_0.3.1
[17] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.1
[18] GenomicFeatures_1.21.30
[19] BSgenome.Hsapiens.UCSC.hg19_1.4.0
[20] BSgenome_1.37.5
[21] rtracklayer_1.29.27
[22] Biostrings_2.37.8
[23] XVector_0.9.4
[24] annotate_1.47.4
[25] XML_3.98-1.3
[26] AnnotationDbi_1.31.18
[27] Biobase_2.29.1
[28] openxlsx_3.0.0
[29] Rsubread_1.19.5
[30] GenomicRanges_1.21.28
[31] GenomeInfoDb_1.5.16
[32] magrittr_1.5
[33] dplyr_0.4.3
[34] foreach_1.4.2
[35] plyr_1.8.3
[36] stringr_1.0.0
[37] IRanges_2.3.21
[38] ggplot2_1.0.1
[39] S4Vectors_0.7.18
[40] BiocGenerics_0.15.6
[41] BiocInstaller_1.19.14
loaded via a namespace (and not attached):
[1] Category_2.35.1 bitops_1.0-6 RColorBrewer_1.1-2
[4] tools_3.2.0 R6_2.1.1 KernSmooth_2.23-15
[7] lazyeval_0.1.10 colorspace_1.2-6 Nozzle.R1_1.1-1
[10] compiler_3.2.0 sendmailR_1.2-1 graph_1.47.2
[13] labeling_0.3 checkmate_1.6.2 caTools_1.17.1
[16] scales_0.3.0 BatchJobs_1.6 genefilter_1.51.1
[19] RBGL_1.45.1 digest_0.6.8 AnnotationForge_1.11.19
[22] base64enc_0.1-3 BBmisc_1.9 GOstats_2.35.1
[25] hwriter_1.3.2 gtools_3.5.0 RCurl_1.96-0
[28] GO.db_3.2.1 futile.logger_1.4.1 Matrix_1.2-2
[31] Rcpp_0.12.1 munsell_0.4.2 proto_0.3-10
[34] stringi_0.5-5 edgeR_3.11.3 MASS_7.3-44
[37] zlibbioc_1.15.0 fail_1.2 gplots_2.17.0
[40] grid_3.2.0 gdata_2.17.0 lattice_0.20-33
[43] splines_3.2.0 rjson_0.2.15 systemPipeR_1.3.43
[46] reshape2_1.4.1 codetools_0.2-14 biomaRt_2.25.3
[49] futile.options_1.0.0 ShortRead_1.27.5 latticeExtra_0.6-26
[52] lambda.r_1.1.7 gtable_0.1.2 amap_0.8-14
[55] assertthat_0.1 chipseq_1.19.1 xtable_1.7-4
[58] survival_2.38-3 pheatmap_1.0.7 brew_1.0-6
[61] GSEABase_1.31.3
Hi Ryan,
ChIPQC()callsdoChIPQCsample()which callsChIPQCsample()which callssampleQC()which callstable()on an RleList object that was obtained withcoverage(). The call totable()happens in ChIPQC/R/sampleQC.R at lines 86-88:Cov <- coverage(Sample_GIT,width=unname(ChrLengths[k])) message("Calculating coverage histogram for ",names(ChrLengths)[k],"\n") CovHist <- c(CovHist,list(colSums(table(Cov))))Calling
table()on an RleList object dispatches on the"table"method for AtomicList objects defined in the IRanges package (there is no specific table method for RleList objects). This method is defined as follow (in IRanges/R/AtomicList-impl.R):### Could actually be made the "table" method for List objects. Will ### work on any List object 'x' for which 'as.factor(unlist(x))' works. setMethod("table", "AtomicList", function(...) { args <- list(...) if (length(args) != 1L) stop("\"table\" method for AtomicList objects ", "can only take one input object") x <- args[[1L]] y1 <- togroup(x) attributes(y1) <- list(levels=as.character(seq_along(x)), class="factor") y2 <- as.factor(unlist(x, use.names=FALSE)) ans <- table(y1, y2) names(dimnames(ans)) <- NULL x_names <- names(x) if (!is.null(x_names)) rownames(ans) <- x_names ans } )As you can see, this method tries to unlist the RleList object and this fails because the resulting object would have a length >= 2^32 (we don't support long Rle objects). This is a known limitation of this
"table"method (see comment at the top). Another problem is that even when it works, it's very inefficient on RleList objects. A much more efficient implementation would be to do something like:## A table() implementation for RleList objects with numerical list ## elements. Work on big objects and is much more efficient than the ## table,AtomicList method. table_RleList <- function(x) { nbins <- max(max(x)) + 1L data <- lapply(x, function(xi) S4Vectors:::tabulate2(runValue(xi) + 1L, nbins, weight=runLength(xi))) ans <- matrix(unlist(data, use.names=FALSE), nrow=length(x), byrow=TRUE) dimnames(ans) <- list(names(x), 0:(nbins-1L)) class(ans) <- "table" ans }Then:
I'll try to integrate
table_RleList()to the IRanges package in the near future (not sure I'll have time to work on this before the next release though).@ChIPQC maintainers: in the meantime you can always copy/paste the definition of
table_RleList()and use it internally instead oftable():Cheers,
H.