From bf959c22b57f8f591b570e8f9fc15abb6c39f9d4 Mon Sep 17 00:00:00 2001 From: lcolladotor Date: Mon, 20 May 2024 23:02:00 -0400 Subject: [PATCH] Try to create space on GHA to avoid running out of space like at https://github.com/LieberInstitute/recountWorkflow/actions/runs/9167737161/job/25205360164#step:15:202. Related to the workaround for https://github.com/lawremi/rtracklayer/issues/83 --- vignettes/recount-workflow.Rmd | 16 +++++++++++++++- 1 file changed, 15 insertions(+), 1 deletion(-) diff --git a/vignettes/recount-workflow.Rmd b/vignettes/recount-workflow.Rmd index b4f0c96..fe16c87 100644 --- a/vignettes/recount-workflow.Rmd +++ b/vignettes/recount-workflow.Rmd @@ -729,7 +729,7 @@ 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$OS.type != 'windows'} +```{r 'download_mean_bigwig', eval = .Platform$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 @@ -754,10 +754,21 @@ table(width(regions) >= 100) ## Keep only the ones that are at least 100 bp long regions <- regions[width(regions) >= 100] length(regions) + +## Remove file we no longer need +unlink("SRP045638/bw", recursive = TRUE) ``` Now that we have a set of regions to work with, we proceed to build a _RangedSummarizedExperiment_ object with the coverage counts, add the expanded metadata we built for the gene-level, and scale the counts. Note that `coverage_matrix()` scales the base-pair coverage counts by default, which we turn off in order to use use `scale_counts()`. +```{r 'download_sample_bigwigs', eval = .Platform$OS.type != 'windows'} +## Normally, one can use rtracklayer::import() to access remote parts of BigWig +## files without having to download the complete files. However, as of +## 2024-05-20 this doesn't seem to be working well. So this is a workaround to +## issue https://github.com/lawremi/rtracklayer/issues/83 +download_study("SRP045638", type = "samples") +``` + ```{r "build_rse_ER", eval = .Platform$OS.type != "windows"} ## Compute coverage matrix for study SRP045638, only for chromosome 21 ## Takes about 4 minutes @@ -774,6 +785,9 @@ rse_er_scaled <- scale_counts(rse_er) ## To highlight that we scaled the counts rm(rse_er) + +## Remove files we no longer need +unlink("SRP045638/bw", recursive = TRUE) ``` Now that we have a scaled count matrix for the expressed regions, we can proceed with the DE analysis just like we did at the gene and exon feature levels (Figures \@ref(fig:erdeanalysis1), \@ref(fig:erdeanalysis2), \@ref(fig:erdeanalysis3), and \@ref(fig:erdeanalysis4)).