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geneToPB.R
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geneToPB.R
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geneToPB<-function(g, pb.granges=hq.gff.transcripts){
require(org.Hs.eg.db)
require(GenomicRanges)
require(GenomicFeatures)
hs<-org.Hs.eg.db
coord<-select(hs, keys = g, columns = c("CHR", "CHRLOC", "CHRLOCEND"), keytype = "SYMBOL")
loci<-GRanges(seqnames = paste("chr", coord$CHR, sep = ""),
ranges = IRanges(start = abs(coord$CHRLOC),
end = abs(coord$CHRLOCEND),
names = g),
strand = ifelse(coord$CHRLOC<0, "-", "+"))
pbloci<-subsetByOverlaps(hq.gff.transcripts, loci)
return(list(GENE = unique(pbloci$gene_id), START = min(start(loci)), END = max(end(loci)), CHR = as.character(unique(seqnames(loci))[1]), STRAND = unique(as.character(strand(loci)))[1]))
}
# pbToGene(pb, pb.granges=hq.gff.transcripts){
# require(org.Hs.eg.db)
# require(GenomicRanges)
# require(GenomicFeatures)
# }