gapfillerWrap {chimera} | R Documentation

## A function to prepare files and to run gapfiller

### Description

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.

### Usage

    gapfillerWrap(chimeraSeqSet.out, bam, parallel=c(FALSE,TRUE))

### Arguments

`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

### Value

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

### Author(s)

Raffaele A Calogero

### See Also

`chimeraSeqs`, `gapfillerInstallation`, `gapfillerRun`

### Examples

    #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))

[Package chimera version 1.22.0 Index]