Comments (2)
I quickly concocted a work around, maybe this is of use to anyone (too much in a hurry to do this a as a proper pull request, sorry :-)
.ensid <- function(gene){
gsub(perl=TRUE, "\\.\\d+$","",
unlist(lapply(strsplit(gene, "\\^"), function(p)p[2])))
}
addEnsemblIds <- function(file, fusions) {
## Specific to STAR-fusion output
## import misses the ens id's, add them here
## Usage: fusions <- addEnsemblIds(file,fusions)
table <- read.table(file=file,
sep="\t", as.is=TRUE, quote="", header=TRUE,
comment.char="", row.names=NULL)
if(nrow(table) != length(fusions))
stop("Number of fusions found in ", file,
" unequal to that in fusions argument")
if (is.null(table$LeftGene) || is.null(table$RightGene))
stop("Missing columns LeftGene and/or RightGene in ", file)
ensA <- .ensid(table$LeftGene)
ensB <- .ensid(table$RightGene)
sapply(1:length(fusions), function(i) {
f <- fusions[[i]]
f@geneA@ensemblId <- ensA[i]
f@geneB@ensemblId <- ensB[i]
f
})
} #addEnsemblIds
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Thank you!:) I've pushed a fix for this which will be available in chimeraviz version 1.4.2 of the release version of Bioconductor, and chimeraviz version 1.5.4 of the devel version of Bioconductor.
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Related Issues (20)
- Question: what are the red bands on the chromosome? HOT 4
- Assignment to global environment HOT 1
- plot_fusion function not finding "SPFQ" or "CADM2" transcripts in an edb object that has them. HOT 2
- Why is it impossible to use plot_fusion_transcript_with_protein_domain without a BAM file? HOT 1
- Support ChimPipe HOT 1
- coverage issue in plot_fusion_separate HOT 2
- How to make fusioncatcher data compatible to chimeraviz HOT 4
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- Support Fusion-Bloom
- Travis build fails
- plot_fusion_transcript_with_protein_domain(): error plotting upstream domains HOT 2
- Failed to create reference fasta file HOT 4
- How to input STAR-SEQR output? HOT 1
- Dependency on deprecated ArgumentCheck CRAN package HOT 1
- 2 question with chimeraviz HOT 3
- Custom genomes HOT 2
- Error during the execution of plot_fusion HOT 5
- Failed to create EnsDb HOT 1
- No coverage data for plot_fusion HOT 2
- Fusion transcript plot with protein domain annotations HOT 1
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