Unlike the other methods, TIMER needs the specification of the cancer type for each sample.
deconvolute_timer(gene_expression_matrix, indications = NULL)a m x n matrix with m genes and n samples
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'