chimera (version 1.14.0)

chimeraSeqSet: 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.

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)})