fusionPeptides {chimera} | R Documentation |
A function extracting the donor and the acceptor peptides involved in the fusion.
fusionPeptides(chimeraSeq.output, annotation="hsUCSC")
chimeraSeq.output |
DNAStringSet encompassing the fusion event of interest, generated by chimeraSeq function |
annotation |
The annotation used to retrieve the UCSC names of the transcripts involved in the fusion |
An list encompassing:
AAStringSet |
encompassing: fusion sequence, peptide from p1 and peptide from p2. In case the peptides are not in frame the AAStringSet will not contain the fusion sequence |
DNAStringSet |
encompassing the fusion transcript |
Raffaele A Calogero
tmp <- importFusionData("fusionmap", paste(find.package(package="chimera"),"/examples/mcf7.FMFusionReport", sep=""), org="hg19") fusion.names <- fusionName(tmp) fusion.names myset <- tmp[1:3] tmp.seq <- chimeraSeqSet(myset, parallel=FALSE) tmpx <- lapply(tmp.seq,fusionPeptides)