GetImmuneContent: GetImmuneContent

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

GetImmuneContent

Description

Estimate the Tissue Immune Microenvironment content based on LM22 signature. It is based on TPMs calculated from the gene counts. duplicated genes will be removed If MIXTURE package is not already installed, it will be installed

Usage

GetImmuneContent(ftc, filter = 0, plot = TRUE)

Arguments

ftc	object returned by GetCounts The ftc should be an object returned by GetCounts called with the parameter feature = "gene" this parameter is saved in ftc$targets[2] position and this function will check this, otherwise it trough an error
filter	(integer) minimal count level to consider (default 0L)
plot	(logical) if TRUE (default) the subject proportion plot, no plot otherwise

Value

a MIXTURE object (see MIXTURE)

Examples

## Not run: 
test.subject <- GetArribaRTest()
bam.subject <- RunSTAR(test.subject)
ft <- GetCounts(bam.subject)
ft.imm <- GetImmuneContent(ft)

## End(Not run)

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