FusionPlot: FusionPlot This function provides gene fusion visualization

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

FusionPlot This function provides gene fusion visualization

Description

FusionPlot This function provides gene fusion visualization

Usage

FusionPlot(sbjBamFile,gene1,gene2)

Arguments

sbjBamFile	string with full path of the processed and sorted bam file processed by RunSTAR and RunArriba
gene1	string with geneID as returned by RunArriba _Fusion.xlsx table. Default missing (will plot all the fusions), otherwise it will only plot all the fusions where this gene is present
gene2	idem as gene1. If both gene1 and gene2 are set, only the fusions including those genes will be plotted
fusions	if missing, it will upload the Fusions.xlsx file, else excel file with the desired fusions should be provided
savePlot	(boolean) if plot should be saved

See Also

runArriba

Examples

## Not run: 
test.subject <- GetArribaRTest()
bam.subject <- RunSTAR(test.subject)
Fusions <- RunArriba(bam.subject)
bam.sorted.subject <- RunSortIndexBam(bam.subject)
FusionPlot(bam.sorted.subject)

## End(Not run)

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