chimeraSeqSet {chimera} | R Documentation

## A function to generates DNAStringSet encompassing fusion sequences

### Description

A function generating the nucleotide sequences of chimeras described in a list of fSet, i.e. the list generated using importFusionData function.

### Usage

    chimeraSeqSet(list, parallel=FALSE)

### Arguments

`list` | A list of fSet objects.
`parallel` | If TRUE uses the BioParallel package

### Value

A DNAStringSet encompassing the fusions described in a list of fSet objects. This object represents the ideal reference to remap reads over detected fusions. Remapping is required to validate fusions using GapFiller de novo reconstruction.

### Author(s)

Raffaele A Calogero

### See Also

`fusionName, importFusionData, gapfillerInstallation, gapfillerRun`

### 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)
    #   sapply(tmp.seq, function(x){writeXStringSet(x, "detected.fusions.fa", format="fasta", append=TRUE)})

[Package chimera version 1.22.0 Index]