immunedeconv (version 2.0.0)

deconvolute_quantiseq: Deconvolute using quanTIseq

Description

Deconvolute using quanTIseq

Usage

deconvolute_quantiseq(gene_expression_matrix, tumor, arrays, scale_mrna,
  ...)

Arguments

gene_expression_matrix

a m x n matrix with m genes and n samples

tumor

Set to TRUE if dealing with a tumor samples. if TRUE, signature genes with high expressin in tumor samles are removed.

arrays

Set to TRUE if working with Microarray data instead of RNA-seq

scale_mrna

Set to FALSE to disable correction for cell type-specific differences in mRNA content

...

passed through to original quantiseq method. A native argument takes precedence over an immunedeconv argument (e.g. mRNAscale takes precedence over scale_mrna) See deconvolute_quantiseq.default().