Entering edit mode
Hi all,
I am trying to get per-base counts over a series of ranges using the
pileupAsGRanges function. I'm only interesting in certain regions for
each bam file, so have written a script to extract the pileup from
each bam file for the regions of interest to that bam (the gr2 object
below, which changes according to bam file).
However, I'm having issues creating pileup from one of my ranges
objects. To my eye, it looks to be a valid GRanges object
> gr2
GRanges with 12 ranges and 4 metadata columns:
seqnames ranges strand |
Sample
<rle> <iranges> <rle> |
<factor>
F1_W chr18 [ 48604746, 48604747] * |
EN-438-11_Blood
F2_W chr2 [125320840, 125320841] * |
EN-438-11_Blood
F3_W chr17 [ 7577114, 7577115] * |
EN-454-12_EXP0628_TF_Blood
F4_W chr1 [ 27099124, 27099125] * |
EN-454-12_EXP0628_TF_Blood
F5_W chr9 [120474984, 120474985] * |
EN-454-12_EXP0628_TF_Blood
F6_W chr1 [248039414, 248039415] * |
EN-454-12_EXP0628_TF_Blood
F7_W chr19 [ 11130352, 11130353] * |
EN-460-12_Blood
F8_W chr19 [ 11141514, 11141515] * |
EN-460-12_Blood
F9_W chr8 [ 89058912, 89058913] * |
EN-460-12_Blood
F10_W chr20 [ 23016541, 23016542] * |
EN-64-10_EXP0628_TF_Blood
F11_W chr10 [118225601, 118225602] * |
EN-64-10_EXP0628_TF_Blood
F12_W chr17 [ 7578188, 7578189] * |
EN-81-10_EXP0628_TF_Blood
Barcode Ref_base Alt_base
<character> <factor> <factor>
F1_W FLD283 G T
F2_W FLD283 T G
F3_W FLD283 C T
F4_W FLD283 G A
F5_W FLD283 C A
F6_W FLD283 G A
F7_W FLD283 T C
F8_W FLD283 A G
F9_W FLD283 C T
F10_W FLD283 A G
F11_W FLD283 A T
F12_W FLD283 C A
> pileupAsGRanges(bam=bams[85],
region=gr2,maxDepth=.Machine$integer.max,minBaseQuality=30,
minMapQuality=30)
Error: applyPileups: invalid 'times' argument
In addition: Warning messages:
1: In start(regions):end(regions) :
numerical expression has 12 elements: only the first used
2: In start(regions):end(regions) :
numerical expression has 12 elements: only the first used
However, the pileup seems to work for each element in the GRanges
object individually if I call them one-by-one without the error or the
warning.
e.g.
> pileupAsGRanges(bam=bams[85],
region=gr2[1,],maxDepth=.Machine$integer.max,minBaseQuality=30,
minMapQuality=30)
GRanges with 2 ranges and 7 metadata columns:
seqnames ranges strand | A C
G
<rle> <iranges> <rle> | <integer> <integer>
<integer>
[1] chr17 [7577539, 7577539] + | 0 0
27
[2] chr17 [7577540, 7577540] + | 0 0
27
T N depth
<integer> <integer> <numeric>
[1] 0 0 27
[2] 0 0 27
bam
<character>
[1] bamfiles/SLX-6363.FLD0187.1093.s_1.bwa.homo_sapiens.bam
[2] bamfiles/SLX-6363.FLD0187.1093.s_1.bwa.homo_sapiens.bam
---
seqlengths:
chr17
NA
I'm struggling to see why the pileup using the whole gr2 object as an
input isn't working.
Thanks a lot,
Mark
> sessionInfo()
R version 2.15.2 (2012-10-26)
Platform: x86_64-pc-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8
[5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8
[7] LC_PAPER=C LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] gdata_2.12.0 biovizBase_1.6.2 Rsamtools_1.10.2
[4] Biostrings_2.26.3 GenomicRanges_1.10.7 IRanges_1.16.6
[7] BiocGenerics_0.4.0
loaded via a namespace (and not attached):
[1] AnnotationDbi_1.20.7 Biobase_2.18.0 biomaRt_2.14.0
[4] bitops_1.0-5 BSgenome_1.26.1 cluster_1.14.2
[7] colorspace_1.2-1 DBI_0.2-5 dichromat_2.0-0
[10] GenomicFeatures_1.10.2 grid_2.15.2 gtools_2.7.0
[13] Hmisc_3.10-1 labeling_0.1 lattice_0.20-10
[16] munsell_0.4 parallel_2.15.2 plyr_1.8
[19] RColorBrewer_1.0-5 RCurl_1.95-4.1 RSQLite_0.11.2
[22] rtracklayer_1.18.2 scales_0.2.3 stats4_2.15.2
[25] stringr_0.6.2 tools_2.15.2 XML_3.95-0.2
[28] zlibbioc_1.4.0
