Return a relative fold change matrix of ATAC peaks for a list of genes

This function returns a relative fold change matrix of ATAC peaks for a list of genes matched using rna_atac_cor_knn.

Usage

get_genes_atac_fp(
  atac_mc,
  genes = NULL,
  metacells = NULL,
  rm_zeros = TRUE,
  spearman = TRUE,
  pairwise.complete.obs = TRUE
)

Arguments

atac_mc

a McPeaks/McTracks object

genes

a list of genes.

rm_zeros

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

spearman

if 'TRUE' Spearman correlation is computed, otherwise Pearson

pairwise.complete.obs

see below

metacell

select only a subset of the metacells.

Examples

if (FALSE) {
marker_genes <- get_rna_markers(atac_mc)
atac_fp <- get_genes_atac_fp(atac_mc, genes = marker_genes)
rna_fp <- get_rna_marker_matrix(atac_mc, genes = marker_genes)
}