Format the mixture matrix before deconvolution

Format the mixture matrix before deconvolution

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)