From 77aab83df246ae22eaae7578a830a3b660e90305 Mon Sep 17 00:00:00 2001 From: bug1303 Date: Thu, 11 Nov 2021 11:44:13 +0100 Subject: [PATCH] fixed regex for is.mito grep for "^MT-" instead of just "MT" to identify mitochondrial genes --- inst/book/tenx-filtered-pbmc3k-4k-8k.Rmd | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/inst/book/tenx-filtered-pbmc3k-4k-8k.Rmd b/inst/book/tenx-filtered-pbmc3k-4k-8k.Rmd index 6b4e4f7..92f5eb4 100644 --- a/inst/book/tenx-filtered-pbmc3k-4k-8k.Rmd +++ b/inst/book/tenx-filtered-pbmc3k-4k-8k.Rmd @@ -37,7 +37,7 @@ library(scater) stats <- high.mito <- list() for (n in names(all.sce)) { current <- all.sce[[n]] - is.mito <- grep("MT", rowData(current)$Symbol_TENx) + is.mito <- grep("^MT-", rowData(current)$Symbol_TENx) stats[[n]] <- perCellQCMetrics(current, subsets=list(Mito=is.mito)) high.mito[[n]] <- isOutlier(stats[[n]]$subsets_Mito_percent, type="higher") all.sce[[n]] <- current[,!high.mito[[n]]]