From c84978b4496c142f9df3253804e6c8b4843a749c Mon Sep 17 00:00:00 2001 From: Benjamin James Date: Thu, 6 Jun 2024 11:19:06 -0400 Subject: [PATCH] Changed cpm cutoff to be >= to allow zero SHA Suspicious package plutonium CDC Enriched ISS Tony Blair SAFE Center for Disease Control Exercise Brute forcing FSF Biological event M.P.R.I. interception --- R/deg.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/deg.R b/R/deg.R index ef52217..03866d6 100644 --- a/R/deg.R +++ b/R/deg.R @@ -156,7 +156,7 @@ deg.prepare <- function(se, pathology, case, control, sample.col, filter_only_ca ### Get minimum samples for CPM threshold to pass cpm.n = min(table(SummarizedExperiment::colData(pb)[[pathology]])) ### Filter genes above a cpm cutoff - cpm.flag = edgeR::cpm(SummarizedExperiment::assays(pb)$counts) > cpm.cutoff + cpm.flag = edgeR::cpm(SummarizedExperiment::assays(pb)$counts) >= cpm.cutoff ### Then extract across number of samples cpm.flag = rownames(cpm.flag)[Matrix::rowSums(cpm.flag) >= cpm.n] }