deconvolute_quantiseq.default: Use quanTIseq to deconvolute a gene expression matrix.

In IOBR/IOBR: Immune Oncology Biological Research

Use quanTIseq to deconvolute a gene expression matrix.

Description

Source code from https://github.com/FFinotello/quanTIseq

Usage

deconvolute_quantiseq.default(
  mix.mat,
  arrays = FALSE,
  signame = "TIL10",
  tumor = FALSE,
  mRNAscale = TRUE,
  method = "lsei",
  rmgenes = "unassigned"
)

Arguments

mix.mat	table with the gene TPM (or microarray expression values) for all samples to be deconvoluted (Gene symbols on the first column and sample IDs on the first row). Expression data must be on non-log scale
arrays	specifies whether expression data are from microarrays (instead of RNA-seq). If TRUE, the "–rmgenes" parameter is set to "none".
signame	name of the signature matrix. Currently only 'TIL10' is available.
tumor	specifies whether expression data are from tumor samples. If TRUE, signature genes with high expression in tumor samples are removed. Default: FALSE.
mRNAscale	specifies whether cell fractions must be scaled to account for cell-type-specific mRNA content. Default: TRUE.
method	deconvolution method to be used: "hampel", "huber", or "bisquare" for robust regression with Huber, Hampel, or Tukey bisquare estimators, respectively, or "lsei" for constrained least squares regression. The fraction of uncharacterized cells ("other") is computed only by the "lsei" method. Default: "lsei".
rmgenes	Default: "default" for RNAseq, "none" for microArray data

Details

F. Finotello, C. Mayer, C. Plattner, G. Laschober, D. Rieder, H. Hackl, A. Krogsdam, W. Posch, D. Wilflingseder, S. Sopper, M. Jsselsteijn, D. Johnsons, Y. Xu, Y. Wang, M. E. Sanders, M. V. Estrada, P. Ericsson-Gonzalez, J. Balko, N. F. de Miranda, Z. Trajanoski. "quanTIseq: quantifying immune contexture of human tumors". bioRxiv 223180. https://doi.org/10.1101/223180.

IOBR/IOBR documentation built on April 4, 2024, 1:07 a.m.