Perform deconvolution on a mouse RNAseq dataset

deconvolute_mouse(
  gene_expression_matrix,
  method = deconvolution_methods_mouse,
  rmgenes = NULL,
  column = "gene_symbol",
  algorithm = NULL,
  ...
)

Arguments

gene_expression_matrix: a m x n matrix with m genes and n samples. Data should be TPM normalized, except when using seqImmuCC where raw counts are prefereable.
method: string specifying the method
rmgenes: noisy genes to be removed from the analysis
column: Only relevant if gene_expression is an ExpressionSet. Defines in which column of fData the HGNC symbol can be found.
algorithm: statistcal algorithm for SeqImmuCC (ignored by all other methods)
...: additional arguments passed to the respective method

Value

a dataset with the estimated fractions/scores, with samples in rows and cell types in column