Hi all, coverage(), naughty boy!
I have two GRanges instances # my 100 million tags > class(B) [1] "GRanges" attr(,"package") [1] "GenomicRanges" # a few ChIP-seq peaks > class(P) [1] "GRanges" attr(,"package") [1] "GenomicRanges" # Now I want to keep only the tags in-peak > BP <- B[B %in% P,] # Are you ok BP? > class(BP) [1] "GRanges" attr(,"package") [1] "GenomicRanges" # Good. # Now, whilst coverage(B) and coverage(P) work, BP crashes > coverage(BP) Error in coverage.normargWidth(width, length(x)) : 'x' has no element and 'width' is NULL BP is, I understand, I subset of B. Why would it crash coverage()? Thank you, Ivan > sessionInfo() R version 2.12.0 Under development (unstable) (2010-03-25 r51410) x86_64-unknown-linux-gnu locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 [4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C [10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] BSgenome.Mmusculus.UCSC.mm9_1.3.16 chipseq_0.3.5 [3] ShortRead_1.5.21 lattice_0.18-3 [5] BSgenome_1.15.19 Biostrings_2.15.25 [7] GenomicRanges_0.0.9 IRanges_1.5.70 [9] rtracklayer_1.7.11 RCurl_1.3-1 [11] bitops_1.0-4.1 loaded via a namespace (and not attached): [1] Biobase_2.6.1 grid_2.12.0 hwriter_1.1 tools_2.12.0 XML_2.6-0 _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
