[Bioc-devel] contradictions in the return value of predictCoding() from VariantAnnotation
Hi Michael, Thanks for reporting the bug and sending a reproducible example. Sorry it took a few days to get to this. A fix has been checked into versions 1.4.12 (release) and 1.5.44 (devel). Valerie
On 03/07/13 05:43, Michael Stadler wrote:
Here is the second attachment ("variants.vcf") that was missing from the
first message.
Michael
On 03/07/2013 02:40 PM, Michael Stadler wrote:
Dear Valerie and colleagues,
I have recently started using the VariantAnnotation package, which is a
huge asset for much of my work with sequence variants - thank you!
I have a question regarding the following example (it makes use of two
small text files, "annot.gtf" and "variants.vcf", attached to this message):
library(VariantAnnotation)
library(GenomicFeatures)
library(BSgenome.Celegans.UCSC.ce6)
# build a TranscriptDb from "annot.gtf"
chrominfo <- data.frame(chrom=as.character(seqnames(Celegans)),
length=seqlengths(Celegans),
is_circular=FALSE)
txdb <- makeTranscriptDbFromGFF(file="annot.gtf",
format="gtf",
chrominfo=chrominfo,
dataSource="WormBase v. WS190",
species="Caenorhabditis elegans")
txdb
#TranscriptDb object:
#| Db type: TranscriptDb
#| Supporting package: GenomicFeatures
#| Data source: WormBase v. WS190
#| Organism: Caenorhabditis elegans
#| miRBase build ID: NA
#| transcript_nrow: 7
#| exon_nrow: 42
#| cds_nrow: 42
#| Db created by: GenomicFeatures package from Bioconductor
#| Creation time: 2013-03-07 14:21:08 +0100 (Thu, 07 Mar 2013)
#| GenomicFeatures version at creation time: 1.11.14
#| RSQLite version at creation time: 0.11.2
#| DBSCHEMAVERSION: 1.0
# read in sequence variants
vcf <- readVcf("variants.vcf", genome="ce6")
dim(vcf)
#[1] 3 1
# predict the impact on coding sequences
aa <- predictCoding(query=vcf, subject=txdb, seqSource=Celegans)
length(aa)
#[1] 7
# My question is related to the impact of variant "chrV:15822727":
# This SNV is overlapping two transcripts (same base, plus strand),
# yet the reported VARCODON values are different (GAT -> TAT/AAT):
aa[names(aa)=="chrV:15822727",c("REF","ALT","varAllele","REFCODON","VARCODON")]
#GRanges with 2 ranges and 5 metadata columns:
# seqnames ranges strand |
# <Rle> <IRanges> <Rle> |
# chrV:15822727 chrV [15822727, 15822727] + |
# chrV:15822727 chrV [15822727, 15822727] + |
# REF ALT varAllele
# <DNAStringSet> <DNAStringSetList> <DNAStringSet>
# chrV:15822727 G A A
# chrV:15822727 G A A
# REFCODON VARCODON
# <DNAStringSet> <DNAStringSet>
# chrV:15822727 GAT TAT
# chrV:15822727 GAT AAT
# ---
# seqlengths:
# chrI chrV
# NA NA
# interestingly, when altering the annotation or the set of variants,
# this contradictions disapears (GAT -> AAT):
vcf2 <- vcf[-1] # remove the first SNV
aa2 <- predictCoding(query=vcf2, subject=txdb, seqSource=Celegans)
length(aa2)
#[1] 5
aa2[names(aa2)=="chrV:15822727",c("REF","ALT","varAllele","REFCODON","VARCODON")]
#GRanges with 2 ranges and 5 metadata columns:
# seqnames ranges strand |
# <Rle> <IRanges> <Rle> |
# chrV:15822727 chrV [15822727, 15822727] + |
# chrV:15822727 chrV [15822727, 15822727] + |
# REF ALT varAllele
# <DNAStringSet> <DNAStringSetList> <DNAStringSet>
# chrV:15822727 G A A
# chrV:15822727 G A A
# REFCODON VARCODON
# <DNAStringSet> <DNAStringSet>
# chrV:15822727 GAT AAT
# chrV:15822727 GAT AAT
# ---
# seqlengths:
# chrI chrV
# NA NA
Do you know why this could be the case?
Regards,
Michael
Here is my envirnoment:
sessionInfo()
R Under development (unstable) (2013-02-25 r62061)
Platform: x86_64-unknown-linux-gnu (64-bit)
locale:
[1] C
attached base packages:
[1] parallel stats graphics grDevices utils datasets
[7] methods base
other attached packages:
[1] BSgenome.Celegans.UCSC.ce6_1.3.19
[2] BSgenome_1.27.1
[3] GenomicFeatures_1.11.14
[4] AnnotationDbi_1.21.12
[5] Biobase_2.19.3
[6] VariantAnnotation_1.5.42
[7] Rsamtools_1.11.21
[8] Biostrings_2.27.11
[9] GenomicRanges_1.11.35
[10] IRanges_1.17.35
[11] BiocGenerics_0.5.6
[12] RColorBrewer_1.0-5
loaded via a namespace (and not attached):
[1] DBI_0.2-5 RCurl_1.95-4.1 RSQLite_0.11.2
[4] XML_3.95-0.1 biomaRt_2.15.0 bitops_1.0-5
[7] rtracklayer_1.19.9 stats4_3.0.0 tools_3.0.0
[10] zlibbioc_1.5.0
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