spelling error

benjamin-james · benjamin-james · commit 6b349e7620c7 · 2025-01-15T12:33:39.000-05:00
diff --git a/R/deg.R b/R/deg.R
@@ -183,7 +183,7 @@ deg.prepare <- function(se, pathology, case, control, sample.col, filter_only_ca
     ### Filter by expression
     pb = pb[edgeR::filterByExpr(pb, group=pathology, min.count=min.count, min.prop=frac_n),]
     if (cpm.cutoff > 0) {
-        pb = pb[filterByCPM(assays(pb)[[1]], group=pb[[pathology]], min.prob=frac_n, min.cpm=cpm.cutoff),]
+        pb = pb[filterByCPM(assays(pb)[[1]], group=pb[[pathology]], min.prop=frac_n, min.cpm=cpm.cutoff),]
     }
     se = se[rownames(pb), SummarizedExperiment::colData(se)[[sample.col]] %in% colnames(pb)]
     cd = SummarizedExperiment::colData(se)

Original file line number	Diff line number	Diff line change
`@@ -183,7 +183,7 @@ deg.prepare <- function(se, pathology, case, control, sample.col, filter_only_ca`
`183`	`183`	`### Filter by expression`
`184`	`184`	`pb = pb[edgeR::filterByExpr(pb, group=pathology, min.count=min.count, min.prop=frac_n),]`
`185`	`185`	`if (cpm.cutoff > 0) {`
`186`		`- pb = pb[filterByCPM(assays(pb)[[1]], group=pb[[pathology]], min.prob=frac_n, min.cpm=cpm.cutoff),]`
	`186`	`+ pb = pb[filterByCPM(assays(pb)[[1]], group=pb[[pathology]], min.prop=frac_n, min.cpm=cpm.cutoff),]`
`187`	`187`	`}`
`188`	`188`	`se = se[rownames(pb), SummarizedExperiment::colData(se)[[sample.col]] %in% colnames(pb)]`
`189`	`189`	`cd = SummarizedExperiment::colData(se)`