deconvolute_mouse: Perform deconvolution on a mouse RNAseq dataset

In grst/immunedeconv: Methods for immune cell deconvolution

Perform deconvolution on a mouse RNAseq dataset

Description

Perform deconvolution on a mouse RNAseq dataset

Usage

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

grst/immunedeconv documentation built on Nov. 10, 2023, 1:33 a.m.