gapfillerWrap {chimera} | R Documentation |
A function that uses GapFiller to confirm, by de novo assembly, the presence of the fusion break point. The function needs as input a list of fusion transcript generated by chimeraSeqSet function and the bam file containing the reads remapped over the fusion transcripts made using subreadRun.
gapfillerWrap(chimeraSeqSet.out, bam, parallel=c(FALSE,TRUE))
chimeraSeqSet.out |
a list of DNAStringSet output from chimeraSeqSet |
bam |
bam file containing the reads remapped over the fusion transcripts using Rsubread |
parallel |
if FALSE FALSE no parallelization, if TRUE TRUE full paralleization, if FALSE TRUE only parallelization for internal funtions |
The program will write in a temporary directory contigs.fasta and contig.stats, which are used to evaluate if the de novo assembly allows the identification of the fusion break point. The function returns for each fusion a list of three objects. The list is returned only in case that some of de novo assemblies cover the breakpoint junction. The list is made of:
contigs |
which is a PairwiseAlignments object |
junction.contigs |
which is a DNAStringSet encompassing the sequences present in the contigs object |
fusion |
which is a DNAStringSet object encompassing the fusion transcript |
Raffaele A Calogero
chimeraSeqs
, gapfillerInstallation
, gapfillerRun
#tmp <- importFusionData("star", "Chimeric.out.junction", org="hg19", min.support=100) #myset <- tmp[1:4] #tmp.seq <- chimeraSeqsSet(myset, type="transcripts") #tmp <- gapfillerWrap(chimeraSeqSet.out=trsx, bam="accepted_hits_mapped.bam", parallel=c(FALSE,TRUE))