chimera (version 1.14.0)

fusionPeptides: A function to investigate the peptides involved in the fusion event.

Description

A function extracting the donor and the acceptor peptides involved in the fusion.

Usage

fusionPeptides(chimeraSeq.output, annotation="hsUCSC")

Arguments

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

Value

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

Examples

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)