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

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