From d6796d014c5f445a536cc9b6b84203f4904f7387 Mon Sep 17 00:00:00 2001 From: lcolladotor Date: Mon, 20 May 2024 19:00:20 -0400 Subject: [PATCH] Introduce a workaround to https://github.com/lawremi/rtracklayer/issues/83 --- vignettes/recount-quickstart.Rmd | 13 +++++++++++-- 1 file changed, 11 insertions(+), 2 deletions(-) diff --git a/vignettes/recount-quickstart.Rmd b/vignettes/recount-quickstart.Rmd index f1adb13..ce14a3e 100644 --- a/vignettes/recount-quickstart.Rmd +++ b/vignettes/recount-quickstart.Rmd @@ -520,11 +520,20 @@ The [recount project](https://jhubiostatistics.shinyapps.io/recount/) also hosts For an annotation-agnostic differential expression analysis, we first need to define the regions of interest. With `r Biocpkg('recount')` we can do so using the `expressed_regions()` function as shown below for the same study we studied earlier. +```{r 'download_bigwigs', eval = .Platform$OS.type != 'windows'} +## Normally, one can use rtracklayer::import() to access remote parts of BigWig +## files without having to download the complete files. However, as of +## 2024-05-20 this doesn't seem to be working well. So this is a workaround to +## issue https://github.com/lawremi/rtracklayer/issues/83 +download_study("SRP009615", type = "mean") +download_study("SRP009615", type = "samples") +``` + ```{r 'define_ers', eval = .Platform$OS.type != 'windows'} ## Define expressed regions for study SRP009615, only for chromosome Y regions <- expressed_regions("SRP009615", "chrY", cutoff = 5L, - maxClusterGap = 3000L + maxClusterGap = 3000L, outdir = "SRP009615" ) ## Briefly explore the resulting regions @@ -539,7 +548,7 @@ Having defined the expressed regions, we can now compute a coverage matrix for t ```{r 'compute_covMat', eval = .Platform$OS.type != 'windows'} ## Compute coverage matrix for study SRP009615, only for chromosome Y -system.time(rse_ER <- coverage_matrix("SRP009615", "chrY", regions)) +system.time(rse_ER <- coverage_matrix("SRP009615", "chrY", regions, outdir = "SRP009615")) ## Explore the RSE a bit dim(rse_ER)