From 53cad49fdf170782696df99a90a4f0e4f4c3ce67 Mon Sep 17 00:00:00 2001 From: lcolladotor Date: Mon, 20 May 2024 21:18:29 -0400 Subject: [PATCH] Don't delete the data from SRP009615 just yet. Wait for the other coverage_matrix() call to run. Related to https://github.com/lawremi/rtracklayer/issues/83 --- vignettes/recount-quickstart.Rmd | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/vignettes/recount-quickstart.Rmd b/vignettes/recount-quickstart.Rmd index ce14a3e..4d69288 100644 --- a/vignettes/recount-quickstart.Rmd +++ b/vignettes/recount-quickstart.Rmd @@ -645,9 +645,6 @@ For an `rse_exon` object, the `rownames()` correspond to the Gencode `gene_id`. download_study("SRP009615", type = "rse-exon") load(file.path("SRP009615", "rse_exon.Rdata")) -## Delete it if you don't need it anymore -unlink("SRP009615", recursive = TRUE) - ## Annotation information rowRanges(rse_exon) @@ -684,7 +681,7 @@ seqlevelsStyle(exons) <- "UCSC" ## Get the count matrix at the exon level for chrY exons_chrY <- keepSeqlevels(exons, "chrY", pruning.mode = "coarse") exonRSE <- coverage_matrix("SRP009615", "chrY", unlist(exons_chrY), - chunksize = 3000 + chunksize = 3000, outdir = "SRP009615" ) exonMatrix <- assays(exonRSE)$counts dim(exonMatrix)