Deconvolute using ConsensusTME.

deconvolute_consensus_tme(
  gene_expression_matrix,
  indications = NULL,
  method = "ssgsea",
  ...
)

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. The method requires at least 2 samples of a certain cancer type. 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'
method: Choose statistical framework to generate the entichment scores. Default: 'ssgsea'. Available methods: 'ssgsea', 'gsva', 'plage', 'zscore', 'singScore'. These mirror the parameter options of GSVA::gsva() with the exception of singScore which leverages singscore::multiScore()
...: passed through to the original ConsensusTME function. A native argument takes precedence over an immunedeconv argument. Documentation can be found at http://consensusTME.org