deconvolute_timer: Deconvolute using TIMER

In grst/immunedeconv: Methods for immune cell deconvolution

Deconvolute using TIMER

Description

Unlike the other methods, TIMER needs the specification of the cancer type for each sample.

Usage

deconvolute_timer(gene_expression_matrix, indications = NULL)

Arguments

gene_expression_matrix	a m x n matrix with m genes and n samples
indications	a n-vector giving and indication string (e.g. 'brca') for each sample. Accepted indications are 'kich', 'blca', 'brca', 'cesc', 'gbm', 'hnsc', 'kirp', 'lgg', 'lihc', 'luad', 'lusc', 'prad', 'sarc', 'pcpg', 'paad', 'tgct', 'ucec', 'ov', 'skcm', 'dlbc', 'kirc', 'acc', 'meso', 'thca', 'uvm', 'ucs', 'thym', 'esca', 'stad', 'read', 'coad', 'chol'

grst/immunedeconv documentation built on Nov. 10, 2023, 1:33 a.m.