quanTIseq: Run quanTIseq deconvolution

In federicomarini/quantiseqr: Quantification of the Tumor Immune contexture from RNA-seq data

Run quanTIseq deconvolution

Description

Run quanTIseq deconvolution

Usage

quanTIseq(currsig, currmix, scaling = TRUE, method = "lsei")

Arguments

currsig	Signature matrix to be used for deconvolution (format: genes by cell types).
currmix	Mixture matrix to be deconvoluted (format: genes by samples).
scaling	Logical value. If set to FALSE, it disables the correction of cell-type-specific mRNA content bias. Default: TRUE
method	Character string, defining the deconvolution method to be used: lsei for constrained least squares regression, hampel, huber, or bisquare for robust regression with Huber, Hampel, or Tukey bisquare estimators, respectively. Default: lsei.

Value

A data.frame of cell fractions, cell types by samples.

Examples

data(dataset_racle)
mixture <- dataset_racle$expr_mat
signature.file <- system.file(
  "extdata", "TIL10_signature.txt", package = "quantiseqr", mustWork = TRUE)
signature <- read.table(signature.file, header = TRUE, sep = "\t", row.names = 1)
# cellfrac <- quantiseqr:::quanTIseq(mixture, signature)

federicomarini/quantiseqr documentation built on Dec. 20, 2024, 2:39 a.m.