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