The footprint is defined as the size-normalized geometric mena of the number of umis per metacells, dvided by the median over all metacells.

mc_compute_fp(mc, us, norm_by_mc_size = T, min_total_umi = 10)

Arguments

mc

a metacell object

us

umi matrix

norm_by_mc_size

normalize by mean total umis and then multiply by median mean mc size (or at least 1000). This means umis per 1000 molecules.

min_total_umi

consider genes with at least min_total_umi total umis