This is fixed in 1.10.8 of biovizBase. That function was totally broken. Consider it deprecated. On Thu, Feb 27, 2014 at 9:29 PM, Michael Lawrence <michafla@gene.com> wrote: > I'll fix this in the morning, but I wanted to note that pileupVariants in > the devel VariantTools is a lot more efficient and outputs a more > appropriate VRanges object. I just need to find a way to make VariantTools > optionally dependent on gmapR, so that it can be installed on Windows. > > > On Thu, Feb 27, 2014 at 5:33 PM, Katherine Yahvah <kyahvah@novuscmd.com>wrote: > >> Hello- >> I'm running into an almost identical problem that was previously posted ( >> https://stat.ethz.ch/pipermail/bioconductor/2013-March/051793.html ) but >> have not found a solution to make the analysis work. >> >> I am trying to use pileupAsGRanges to generate the base counts at each >> nucleotide position in a GRanges object. My GRanges object: >> > gr >> GRanges with 225 ranges and 1 metadata column: >> seqnames ranges strand | seqinfo >> <rle> <iranges> <rle> | <integer> >> [1] chr1 [ 4367322, 4367323] * | 1 >> [2] chr1 [14155401, 14155402] * | 2 >> [3] chr1 [14996653, 14996654] * | 3 >> [4] chr1 [34155500, 34155501] * | 4 >> [5] chr1 [54195017, 54195018] * | 5 >> ... ... ... ... ... ... >> [221] chr22 [43579707, 43579708] * | 221 >> [222] chr22 [47836411, 47836412] * | 222 >> [223] chr22 [48362289, 48362290] * | 223 >> [224] chrY [ 8619537, 8619538] * | 224 >> [225] chrY [14096576, 14096577] * | 225 >> --- >> seqlengths: >> chr1 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr2 >> chr20 chr21 chr22 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chrY >> NA NA NA NA NA NA NA NA NA NA NA NA >> NA NA NA NA NA NA NA NA NA NA NA >> >> >> However, when I try to run pileupAsGRanges I get an error: >> >> > >> >> test<-pileupAsGRanges(bam=fls,regions=gr,maxDepth=.Machine$integer. max,minBa >> seQuality=30, minMapQuality=30) >> Error: applyPileups: invalid 'times' argument >> In addition: Warning messages: >> 1: In start(regions):end(regions) : >> numerical expression has 225 elements: only the first used >> 2: In start(regions):end(regions) : >> numerical expression has 225 elements: only the first used >> >> If I run the command with only one element of the GRanges object the >> function works: >> >> > >> >> test<-pileupAsGRanges(bam=fls,regions=gr[1],maxDepth=.Machine$integ er.max,mi >> nBaseQuality=30, minMapQuality=30) >> > test >> GRanges with 2 ranges and 7 metadata columns: >> seqnames ranges strand | A C G >> T N depth bam >> <rle> <iranges> <rle> | <integer> <integer> <integer> >> <integer> <integer> <numeric> <character> >> [1] chr1 [4367322, 4367322] + | 233 0 1 >> 0 0 234 ./IonXpress_001_rawlib.bam >> [2] chr1 [4367323, 4367323] + | 467 0 0 >> 0 0 467 ./IonXpress_001_rawlib.bam >> --- >> seqlengths: >> chr1 >> NA >> >> Any help to figure out how to correct or work around this problem would be >> greatly appreciated. >> Regards, >> Katherine Yahvah >> Research Scientist >> Kashi Clinical Laboratories >> Portland, OR >> >> > sessionInfo() >> R version 3.0.2 (2013-09-25) >> Platform: x86_64-w64-mingw32/x64 (64-bit) >> >> locale: >> [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United >> States.1252 LC_MONETARY=English_United States.1252 >> [4] LC_NUMERIC=C LC_TIME=English_United >> States.1252 >> >> attached base packages: >> [1] grid parallel stats graphics grDevices utils datasets >> methods base >> >> other attached packages: >> [1] BSgenome.Hsapiens.UCSC.hg19_1.3.19 ChIPpeakAnno_2.10.0 >> GenomicFeatures_1.14.3 >> [4] limma_3.18.13 org.Hs.eg.db_2.10.1 >> GO.db_2.10.1 >> [7] RSQLite_0.11.4 DBI_0.2-7 >> AnnotationDbi_1.24.0 >> [10] BSgenome.Ecoli.NCBI.20080805_1.3.17 BSgenome_1.30.0 >> multtest_2.18.0 >> [13] Biobase_2.22.0 biomaRt_2.18.0 >> VennDiagram_1.6.5 >> [16] Rsamtools_1.14.3 Biostrings_2.30.1 >> biovizBase_1.10.7 >> [19] BiocInstaller_1.12.0 GenomicRanges_1.14.4 >> XVector_0.2.0 >> [22] IRanges_1.20.6 BiocGenerics_0.8.0 >> >> loaded via a namespace (and not attached): >> [1] bitops_1.0-6 cluster_1.14.4 colorspace_1.2-4 >> dichromat_2.0-0 Formula_1.1-1 Hmisc_3.14-1 labeling_0.2 >> >> [8] lattice_0.20-24 latticeExtra_0.6-26 MASS_7.3-29 >> munsell_0.4.2 plyr_1.8 RColorBrewer_1.0-5 RCurl_1.95-4.1 >> >> [15] rtracklayer_1.22.3 scales_0.2.3 splines_3.0.2 >> stats4_3.0.2 stringr_0.6.2 survival_2.37-7 tools_3.0.2 >> >> [22] XML_3.98-1.1 zlibbioc_1.8.0 >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > [[alternative HTML version deleted]]