deconvolute_xcell

a m x n matrix with m genes and n samples

gene_expression_matrix

Set to TRUE if microarray data, to FALSE for RNASeq (<code>rnaseq</code> parameter in xCell)

arrays

a character list of the cell types to use
in the analysis. If NULL runs xCell with all cell types.
The spillover compensation step may over compensate, thus it is always better
to run xCell with a list of cell types that are expected to be in the mixture.
The names of cell types in this list must be a subset of the cell types that are inferred by xCell.
(<code>cell.types.use</code> parameter in xCell)

expected_cell_types

Passed through to original xCell function. A native argument takes precedence
over an immunedeconv argument (e.g. <code>rnaseq</code> takes precedence over <code>arrays</code>)
See <a href="/link/xCellAnalysis?package=immunedeconv&version=2.0.0" data-mini-rdoc="immunedeconv::xCellAnalysis">xCellAnalysis</a>

Collection of methods for immune cell deconvolution from bulk RNA-seq samples

Gregor Sturm

immunedeconv

Methods for immune cell deconvolution

deconvolute_xcell function

Passed through to original xCell function. A native argument takes precedence
over an immunedeconv argument (e.g. <code>rnaseq</code> takes precedence over <code>arrays</code>)
See <a href='https://rdrr.io/github/dviraran/xCell/man/xCellAnalysis.html'>xCellAnalysis</a>

deconvolute_xcell: Deconvolute using xCell

Description

Usage

Arguments