fusionPeptides {chimera} | R Documentation

## 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

### 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)

[Package chimera version 1.26.0 Index]