From 9a19e03df4cccf33b562b014353e51de297ebb48 Mon Sep 17 00:00:00 2001 From: lcolladotor Date: Mon, 20 May 2024 19:06:57 -0400 Subject: [PATCH] Workaround to https://github.com/lawremi/rtracklayer/issues/83 --- vignettes/recount-workflow.Rmd | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/vignettes/recount-workflow.Rmd b/vignettes/recount-workflow.Rmd index a166245..d66cdb6 100644 --- a/vignettes/recount-workflow.Rmd +++ b/vignettes/recount-workflow.Rmd @@ -729,6 +729,15 @@ recount2 provides bigWig coverage files (unscaled) for all samples, as well as a For illustrative purposes, we will use the data from chromosome 21 for the SRP045638 project. First, we obtain the expressed regions using a relatively high mean cutoff of 5. We then filter the regions to keep only the ones longer than 100 base-pairs to shorten the time needed for running `coverage_matrix()`. +```{r 'download_bigwigs', eval = .Platform$OS.type != 'windows'} +## Normally, one can use rtracklayer::import() to access remote parts of BigWig +## files without having to download the complete files. However, as of +## 2024-05-20 this doesn't seem to be working well. So this is a workaround to +## issue https://github.com/lawremi/rtracklayer/issues/83 +download_study("SRP045638", type = "mean") +download_study("SRP045638", type = "samples") +``` + ```{r "identify regions", eval = .Platform$OS.type != "windows"} ## Define expressed regions for study SRP045638, only for chromosome 21 regions <- expressed_regions("SRP045638", "chr21",