RunAnalysis: RunAnalysis

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

RunAnalysis

Description

An all in one line to run STAR+Arriba+MIXTURE

Usage

RunAnalysis(sbjFile, feature, immuneTME = TRUE)

Arguments

sbjFile	(character) full path to the first fasta file from a subject (subject_1.fastq or subject_1.fastq.gz ), the scond read file should be subject_2.fastq
feature	(character) "exon" or "gene". it will be overwritten with "gene" if immuneTME == TRUE
immuneTME	(logical (default TRUE) should the MIXTURE algorithm be run?

Value

a list with the following slots:

Fusions : a Gene Fusion data (also in an excel file see RunArriba)

Counts : a list as returned by GetCounts

iTME : immune tumor microenvironment objets as returned by GetImmuneContent

Examples

## Not run: 
results <- RunAnalysis(sbjFile = subject_1.fastq.gz)
##if a do not want to run TME and get the exon counts
results <- RunAnalysis(sbjFile = subject_1.fastq.gz, feature = "exon" , immuneTME = FALSE)

## End(Not run)

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