From 7c3f1f9fb23950f0da74510365919ef5488a3f0b Mon Sep 17 00:00:00 2001 From: lcolladotor Date: Mon, 20 May 2024 22:55:52 -0400 Subject: [PATCH] Add missing pieces to bypass https://github.com/lawremi/rtracklayer/issues/83 for now --- vignettes/recount-workflow.Rmd | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/vignettes/recount-workflow.Rmd b/vignettes/recount-workflow.Rmd index d66cdb6..b4f0c96 100644 --- a/vignettes/recount-workflow.Rmd +++ b/vignettes/recount-workflow.Rmd @@ -742,7 +742,8 @@ download_study("SRP045638", type = "samples") ## Define expressed regions for study SRP045638, only for chromosome 21 regions <- expressed_regions("SRP045638", "chr21", cutoff = 5L, - maxClusterGap = 3000L + maxClusterGap = 3000L, + outdir = "SRP045638" ) ## Explore the resulting expressed regions @@ -761,7 +762,8 @@ Now that we have a set of regions to work with, we proceed to build a _RangedSum ## Compute coverage matrix for study SRP045638, only for chromosome 21 ## Takes about 4 minutes rse_er <- coverage_matrix("SRP045638", "chr21", regions, - chunksize = 2000, verboseLoad = FALSE, scale = FALSE + chunksize = 2000, verboseLoad = FALSE, scale = FALSE, + outdir = "SRP045638" ) ## Use the expanded metadata we built for the gene model