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

In chimera: A package for secondary analysis of fusion products

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

Author(s)

Raffaele A Calogero

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)

chimera documentation built on Nov. 8, 2020, 5:16 p.m.