chimeraSeqSet {chimera} | R Documentation |
A function generating the nucleotide sequences of chimeras described in a list of fSet, i.e. the list generated using importFusionData function.
chimeraSeqSet(list, parallel=FALSE)
list |
A list of fSet objects. |
parallel |
If TRUE uses the BioParallel package |
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.
Raffaele A Calogero
fusionName, importFusionData, gapfillerInstallation, gapfillerRun
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)})