Get the normalized RNA expression matrix (egc) from a McPeaks object

Get RNA expression data, normalized by the total RNA expression in each metacell.

Usage

get_rna_egc(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 RNA expression values for each gene (rows) and metacell (columns)

Examples

if (FALSE) {
rna_mat <- get_rna_egc(atac_mc)
rna_mat <- get_rna_egc(atac_mc, genes = c("MESP1", "MESP2", "PF4"))
rna_mat <- get_rna_egc(atac_mc, rm_zeros = FALSE)
}