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

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'