gset_get_feat_mat: extract umi matrix for the genes in the set, possibly...

In tanaylab/metacell: Meta cell analysis for single cell RNA-seq data

extract umi matrix for the genes in the set, possibly donwsampling

Description

extract umi matrix for the genes in the set, possibly donwsampling

Usage

gset_get_feat_mat(
  gset_id,
  mat_id,
  downsamp = F,
  add_non_dsamp = F,
  downsample_n = NA,
  gene_names_src_targ = NULL
)

Arguments

gset_id	gene set in scdb
mat_id	mat in scdb
downsamp	if this is true the returned matrix is downsampled
downsample_n	number of umis for downsampling (if this is NA, the system will pick up the default heuristic)
gene_names_src_targ	string pair, defining how to convert gene nmaes from the original matrix to the naming scheme of the returned matrix (NA by default, in which case no conversion will be done)
add_non+dsamp	should cells with fewer umis than the downsampling threshold be added to hte matrix with their raw data

tanaylab/metacell documentation built on Jan. 29, 2025, 1:34 a.m.