RunARRIBA: RunARRIBA this function will run the gene fusion detection...

In elmerfer/ArribaR: gene Expression quantification, Gene Fusion detection and Immuno Content Deconvolution by STAR and ARRIBA softwares

RunARRIBA this function will run the gene fusion detection ARRIBA software

Description

RunARRIBA this function will run the gene fusion detection ARRIBA software

Usage

RunARRIBA(sbjBamFile, allProteinPredictions = FALSE)

Arguments

sbjBamFile	string with the full file name of the subject BAM file
allProteinPredictions	if TRUE it will generate all the prediction of the discarded file. It may generate a very big discarded file. it is similar to set -X in the Arriba software

Value

a data frame with the identified fusions https://arriba.readthedocs.io/en/latest/output-files/see details in Arriba output files

References

https://genome.cshlp.org/content/early/2021/02/11/gr.257246.119Uhrig et al.

See Also

runSTAR()

Examples

## Not run: 
test.subject <- GetArribaRTest()
bam.subject <- RunSTAR(test.subject)
Fusions <- RunARRIBA(bam.subject)
View(Fusions)

## End(Not run)

elmerfer/ArribaR documentation built on Nov. 14, 2023, 1 p.m.