gapfillerWrap: A function to prepare files and to run gapfiller
In chimera: A package for secondary analysis of fusion products

Description Usage Arguments Value Author(s) See Also Examples

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.

1	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))

chimera documentation built on Nov. 8, 2020, 5:16 p.m.