ApplyCountThreshold: Remove rare and ubiquitous genes

In mkarikom/RSoptSC: Low-Rank Factorization for Subspace-clustering

Remove rare and ubiquitous genes

Description

This is based on Kiselev et al 2017 (SC3). We remove genes where we observe at least countL copies in less than X

Usage

ApplyCountThreshold(M, countL = 1, countU = 3, X = 3)

Arguments

M	a matrix of expression values for each gene (rows) and cell (columns)
countL	the definition of "expressed" raw counts for lower threshold
countU	the definition of "expressed" raw counts for upper threshold
X	the threshold percentage: lower = X%, upper = 100-X%

Value

indices of genes to keep

mkarikom/RSoptSC documentation built on May 10, 2023, 1:10 a.m.