Get enrichment of normalized counts of gene expression over the median

The function first transforms the UMI matrix to fractions per metacell, and then calculates the enrichment of each gene over the median (dividing the gene expression by the median).

Usage

get_rna_fp(atac_mc, genes = NULL, rm_zeros = TRUE, epsilon = 0.00001)

Arguments

atac_mc

a McPeaks/McTracks object with RNA expression (using add_mc_rna)

genes

list of genes to match. Default (NULL): all genes

rm_zeros

remove genes with no RNA expression in any metacell. Default: TRUE

epsilon

regularization factor added to the log normalized expression

Value

a matrix with normalized counts of gene expression for each gene (rows) and metacell (columns)

Examples

if (FALSE) {
get_rna_fp(atac_mc)
get_rna_fp(atac_mc, "GNLY")
get_rna_fp(atac_mc, "GNLY", epsilon = NULL)
}