fixMixture: Format the mixture matrix before deconvolution

In federicomarini/quantiseqr: Quantification of the Tumor Immune contexture from RNA-seq data

Format the mixture matrix before deconvolution

Description

Format the mixture matrix before deconvolution

Usage

fixMixture(mix.mat, arrays = FALSE)

Arguments

mix.mat	Matrix or data.frame with RNA-seq gene TPM or microarray expression values for all samples to be deconvoluted, with gene symbols as row names and sample IDs as column names. Expression levels should be on non-log scale.
arrays	Logical value. Should be set to TRUE if the expression data are from microarrays. For RNA-seq data, this has to be FALSE (default value).

Value

The input matrix transformed to the natural scale (if needed), with fixed gene names on the rows, and TPM (for RNA-seq) or quantile (for microarrays) normalized.

Examples

data(dataset_racle)
# mixture.fix <- quantiseqr:::fixMixture(dataset_racle$expr_mat)

federicomarini/quantiseqr documentation built on Dec. 20, 2024, 2:39 a.m.