runArriba: Run Arriba on RNA-Seq samples using structural-variants...

In J0bbie/R2CPCT: Misc. functions to perform import and analysis of WGS and RNA-Seq samples

Description

Run Arriba on RNA-Seq samples using structural-variants information derived from WGS.

Usage

runArriba(data.SV, minTAF = 0.05, bamFolder, outputFolder)

Arguments

data.SV	(GRanges): GRanges of SV derived from WGS.
minTAF	(integer): Min. TAF of SV to take into the analysis, set to zero (0) for no filtering.
bamFolder	(character): Path to folder containing the RNA-Seq BAM files (STAR).
outputFolder	(character): Path to folder to write Arriba output.

Value

(chr) Command to run Arriba.

Author(s)

Job van Riet [e-mail]

See Also

Other RNA-Seq: importArriba(), retrieveDESeq2Results()

Examples

	runArriba(
	  data.SV = DR71.CohortWGS$structuralVariants,
	  minTAF = 0.05,
	  bamFolder = '/mnt/data2/hartwig/DR71/Oct2020/dataHMF/RNASeq/BAM/',
	  outputFolder = '/mnt/data2/hartwig/DR71/Oct2020/dataHMF/RNASeq/Arriba/'
	)

J0bbie/R2CPCT documentation built on Feb. 24, 2022, 8:15 a.m.