chimeraSeqSet: A function to generates DNAStringSet encompassing fusion...

Description Usage Arguments Value Author(s) See Also Examples

View source: R/chimeraSeqs.R

Description

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

Usage

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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

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	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)})

Bioconductor-mirror/chimera documentation built on June 1, 2017, 5:30 a.m.