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)
M | a matrix of expression values for each gene (rows) and cell (columns) |
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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% |
indices of genes to keep