diff --git a/DESCRIPTION b/DESCRIPTION
index 2700950..f35ef50 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -76,5 +76,5 @@ URL: https://github.com/leekgroup/recount
BugReports: https://support.bioconductor.org/t/recount/
biocViews: Coverage, DifferentialExpression, GeneExpression, RNASeq, Sequencing,
Software, DataImport, ImmunoOncology
-RoxygenNote: 7.1.1
+RoxygenNote: 7.2.3
Roxygen: list(markdown = TRUE)
diff --git a/R/add_metadata.R b/R/add_metadata.R
index 8961f9a..e3de09a 100644
--- a/R/add_metadata.R
+++ b/R/add_metadata.R
@@ -61,8 +61,9 @@
#' ## Obtain all the recount_brain_v2 metadata if you want to
#' ## explore the metadata manually
#' recount_brain_v2 <- add_metadata(source = "recount_brain_v2")
-add_metadata <- function(rse, source = "recount_brain_v2", is_tcga = FALSE,
- verbose = TRUE) {
+add_metadata <- function(
+ rse, source = "recount_brain_v2", is_tcga = FALSE,
+ verbose = TRUE) {
stopifnot(length(source) == 1)
## For a NOTE in R CMD check
diff --git a/R/add_predictions.R b/R/add_predictions.R
index 6e59c70..85a576d 100644
--- a/R/add_predictions.R
+++ b/R/add_predictions.R
@@ -65,21 +65,22 @@
#'
#' ## Download all the latest predictions
#' PredictedPhenotypes <- add_predictions()
-add_predictions <- function(rse, is_tcga = FALSE, version = "latest",
- verbose = TRUE) {
-
+add_predictions <- function(
+ rse, is_tcga = FALSE, version = "latest",
+ verbose = TRUE) {
## For a NOTE in R CMD check
PredictedPhenotypes <- NULL
if (version == "latest") {
- version <- tryCatch(suppressWarnings(readLines(
- "https://raw.githubusercontent.com/leekgroup/recount-website/master/predictions/latestVersion.txt"
- ))[1],
- error = function(e) {
- print(e)
- v <- "0.0.05"
- message(paste(Sys.time(), "Failed to check the latest version, using version", v))
- return(v)
- }
+ version <- tryCatch(
+ suppressWarnings(readLines(
+ "https://raw.githubusercontent.com/leekgroup/recount-website/master/predictions/latestVersion.txt"
+ ))[1],
+ error = function(e) {
+ print(e)
+ v <- "0.0.05"
+ message(paste(Sys.time(), "Failed to check the latest version, using version", v))
+ return(v)
+ }
)
}
diff --git a/R/coverage_matrix.R b/R/coverage_matrix.R
index e1e98cc..f6556b9 100644
--- a/R/coverage_matrix.R
+++ b/R/coverage_matrix.R
@@ -68,9 +68,10 @@
#' ## One row per region
#' identical(length(regions), nrow(rse))
#' }
-coverage_matrix <- function(project, chr, regions, chunksize = 1000,
- bpparam = NULL, outdir = NULL, chrlen = NULL, verbose = TRUE,
- verboseLoad = verbose, scale = TRUE, round = FALSE, ...) {
+coverage_matrix <- function(
+ project, chr, regions, chunksize = 1000,
+ bpparam = NULL, outdir = NULL, chrlen = NULL, verbose = TRUE,
+ verboseLoad = verbose, scale = TRUE, round = FALSE, ...) {
## Check inputs
stopifnot(is.character(project) & length(project) == 1)
stopifnot(is.character(chr) & length(chr) == 1)
diff --git a/R/download_retry.R b/R/download_retry.R
index b9c65a9..cb5c582 100644
--- a/R/download_retry.R
+++ b/R/download_retry.R
@@ -26,8 +26,9 @@
#' download_retry(
#' recount_url$url[which(recount_url$file_name == "files_info.tsv")[1]]
#' )
-download_retry <- function(url, destfile = basename(url), mode = "wb",
- N.TRIES = 3L, ...) {
+download_retry <- function(
+ url, destfile = basename(url), mode = "wb",
+ N.TRIES = 3L, ...) {
## Based on http://bioconductor.org/developers/how-to/web-query/
## and downloader::download()
diff --git a/R/download_study.R b/R/download_study.R
index 9d67c34..518c8eb 100644
--- a/R/download_study.R
+++ b/R/download_study.R
@@ -99,8 +99,9 @@
#' expect_equivalent(rse_gene, rse_gene_SRP009615)
#' }
#'
-download_study <- function(project, type = "rse-gene", outdir = project,
- download = TRUE, version = 2, ...) {
+download_study <- function(
+ project, type = "rse-gene", outdir = project,
+ download = TRUE, version = 2, ...) {
## Check inputs
stopifnot(is.character(project) & length(project) == 1)
stopifnot(version %in% c(1, 2))
diff --git a/R/expressed_regions.R b/R/expressed_regions.R
index 750223a..dc5c3f7 100644
--- a/R/expressed_regions.R
+++ b/R/expressed_regions.R
@@ -54,8 +54,9 @@
#' single <- unlist(GRangesList(regs))
#' }
#'
-expressed_regions <- function(project, chr, cutoff, outdir = NULL,
- maxClusterGap = 300L, chrlen = NULL, verbose = TRUE, ...) {
+expressed_regions <- function(
+ project, chr, cutoff, outdir = NULL,
+ maxClusterGap = 300L, chrlen = NULL, verbose = TRUE, ...) {
## Check inputs
stopifnot(is.character(project) & length(project) == 1)
stopifnot(is.character(chr) & length(chr) == 1)
diff --git a/R/geo_info.R b/R/geo_info.R
index 04f5440..ee16c53 100644
--- a/R/geo_info.R
+++ b/R/geo_info.R
@@ -25,8 +25,9 @@
#'
#' @examples
#' geo_info("GSM836270")
-geo_info <- function(geoid, verbose = FALSE, sleep = 1 / 2, getGPL = FALSE,
- destdir = tempdir(), ...) {
+geo_info <- function(
+ geoid, verbose = FALSE, sleep = 1 / 2, getGPL = FALSE,
+ destdir = tempdir(), ...) {
if (is.na(geoid)) {
return(NULL)
}
diff --git a/R/scale_counts.R b/R/scale_counts.R
index 49387e6..5f8e677 100644
--- a/R/scale_counts.R
+++ b/R/scale_counts.R
@@ -67,9 +67,9 @@
#' identical(rse_gene, rse_gene_SRP009615)
#' }
#'
-scale_counts <- function(rse, by = "auc", targetSize = 4e7, L = 100,
- factor_only = FALSE, round = TRUE) {
-
+scale_counts <- function(
+ rse, by = "auc", targetSize = 4e7, L = 100,
+ factor_only = FALSE, round = TRUE) {
## Check inputs
stopifnot(is(rse, "RangedSummarizedExperiment"))
stopifnot(length(targetSize) == 1)
diff --git a/README.Rmd b/README.Rmd
index 0b2bd35..0c469ca 100644
--- a/README.Rmd
+++ b/README.Rmd
@@ -16,17 +16,18 @@ knitr::opts_chunk$set(
# recount 
-[](https://www.tidyverse.org/lifecycle/#stable)
+[](https://lifecycle.r-lib.org/articles/stages.html#stable)
[](https://bioconductor.org/checkResults/release/bioc-LATEST/recount)
[](https://bioconductor.org/checkResults/devel/bioc-LATEST/recount)
-[](https://codecov.io/gh/leekgroup/recount?branch=master)
-[](https://github.com/leekgroup/recount/actions)
-[](https://github.com/leekgroup/recount/issues)
[](http://bioconductor.org/packages/stats/bioc/recount/)
[](https://support.bioconductor.org/tag/recount)
[](https://bioconductor.org/packages/release/bioc/html/recount.html#since)
[](http://bioconductor.org/checkResults/devel/bioc-LATEST/recount/)
[](https://bioconductor.org/packages/release/bioc/html/recount.html#since)
+[](https://codecov.io/gh/leekgroup/recount?branch=devel)
+[](https://github.com/leekgroup/recount/actions)
+[](https://github.com/leekgroup/recount/issues)
+[](https://github.com/leekgroup/recount/pulls)
Explore and download data from the recount project available at the [recount2 website](https://jhubiostatistics.shinyapps.io/recount/). Using the `recount` package you can download _RangedSummarizedExperiment_ objects at the gene, exon or exon-exon junctions level, the raw counts, the phenotype metadata used, the urls to the sample coverage bigWig files or the mean coverage bigWig file for a particular study. The _RangedSummarizedExperiment_ objects can be used by different packages for performing differential expression analysis. Using [derfinder](http://bioconductor.org/packages/derfinder) you can perform annotation-agnostic differential expression analyses with the data from the recount project.
diff --git a/README.md b/README.md
index 4b41cbd..26f9978 100644
--- a/README.md
+++ b/README.md
@@ -6,17 +6,11 @@
[](https://www.tidyverse.org/lifecycle/#stable)
+stable](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://lifecycle.r-lib.org/articles/stages.html#stable)
[](https://bioconductor.org/checkResults/release/bioc-LATEST/recount)
[](https://bioconductor.org/checkResults/devel/bioc-LATEST/recount)
-[](https://codecov.io/gh/leekgroup/recount?branch=master)
-[](https://github.com/leekgroup/recount/actions)
-[](https://github.com/leekgroup/recount/issues)
[](http://bioconductor.org/packages/stats/bioc/recount/)
[](https://bi
commit](https://bioconductor.org/shields/lastcommit/devel/bioc/recount.svg)](http://bioconductor.org/checkResults/devel/bioc-LATEST/recount/)
[](https://bioconductor.org/packages/release/bioc/html/recount.html#since)
+[](https://codecov.io/gh/leekgroup/recount?branch=devel)
+[](https://github.com/leekgroup/recount/actions)
+[](https://github.com/leekgroup/recount/issues)
+[](https://github.com/leekgroup/recount/pulls)
Explore and download data from the recount project available at the
@@ -69,7 +71,6 @@ Please run this yourself to check for any updates on how to cite
``` r
print(citation("recount"), bibtex = TRUE)
-#>
#> To cite package 'recount' in publications use:
#>
#> Collado-Torres L, Nellore A, Kammers K, Ellis SE, Taub MA, Hansen KD,
@@ -128,7 +129,7 @@ print(citation("recount"), bibtex = TRUE)
#> Jaffe AE, Langmead B, Leek JT (2023). _Explore and download data from
#> the recount project_. doi:10.18129/B9.bioc.recount
#> ,
-#> https://github.com/leekgroup/recount - R package version 1.25.1,
+#> https://github.com/leekgroup/recount - R package version 1.27.0,
#> .
#>
#> A BibTeX entry for LaTeX users is
@@ -138,7 +139,7 @@ print(citation("recount"), bibtex = TRUE)
#> author = {Leonardo Collado-Torres and Abhinav Nellore and Kai Kammers and Shannon E. Ellis and Margaret A. Taub and Kasper D. Hansen and Andrew E. Jaffe and Ben Langmead and Jeffrey T. Leek},
#> year = {2023},
#> url = {http://www.bioconductor.org/packages/recount},
-#> note = {https://github.com/leekgroup/recount - R package version 1.25.1},
+#> note = {https://github.com/leekgroup/recount - R package version 1.27.0},
#> doi = {10.18129/B9.bioc.recount},
#> }
#>
@@ -218,7 +219,7 @@ By contributing to this project, you agree to abide by its terms.
*[rcmdcheck](https://CRAN.R-project.org/package=rcmdcheck)* customized
to use [Bioconductor’s docker
containers](https://www.bioconductor.org/help/docker/) and
- *[BiocCheck](https://bioconductor.org/packages/3.16/BiocCheck)*.
+ *[BiocCheck](https://bioconductor.org/packages/3.17/BiocCheck)*.
- Code coverage assessment is possible thanks to
[codecov](https://codecov.io/gh) and
*[covr](https://CRAN.R-project.org/package=covr)*.
@@ -234,7 +235,7 @@ By contributing to this project, you agree to abide by its terms.
For more details, check the `dev` directory.
This package was developed using
-*[biocthis](https://bioconductor.org/packages/3.16/biocthis)*.
+*[biocthis](https://bioconductor.org/packages/3.17/biocthis)*.
## Teams involved
diff --git a/dev/02_git_github_setup.R b/dev/02_git_github_setup.R
index ae70cf8..91ea4f6 100644
--- a/dev/02_git_github_setup.R
+++ b/dev/02_git_github_setup.R
@@ -34,7 +34,7 @@ rstudioapi::restartSession()
## Now run use_github()
usethis::use_github()
## Follow any prompts, such as running on the terminal:
-## git push --set-upstream origin master
+## git push --set-upstream origin devel
## Move to the next step: setting up your package core files
diff --git a/dev/03_core_files.R b/dev/03_core_files.R
index b136031..a0c605f 100644
--- a/dev/03_core_files.R
+++ b/dev/03_core_files.R
@@ -9,7 +9,7 @@ rstudioapi::navigateToFile(usethis::proj_path("dev", "02_git_github_setup.R"))
## Check http://r-pkgs.had.co.nz/description.html for details
## as well as http://bioconductor.org/developers/package-guidelines/#description
-## Check https://github.com/lcolladotor/biocthis/blob/master/DESCRIPTION
+## Check https://github.com/lcolladotor/biocthis/blob/devel/DESCRIPTION
## for an example.
## You'll at least want to edit the version to 0.99.0 (or lower) since that's
diff --git a/man/recount-package.Rd b/man/recount-package.Rd
index 553b286..7d5401a 100644
--- a/man/recount-package.Rd
+++ b/man/recount-package.Rd
@@ -6,18 +6,9 @@
\alias{recount-package}
\title{recount: Explore and download data from the recount project}
\description{
-\if{html}{\figure{logo.png}{options: align='right' alt='logo' width='120'}}
+\if{html}{\figure{logo.png}{options: style='float: right' alt='logo' width='120'}}
-Explore and download data from the recount project available at
- https://jhubiostatistics.shinyapps.io/recount/. Using the recount package you can
- download RangedSummarizedExperiment objects at the gene, exon or exon-exon junctions level,
- the raw counts, the phenotype metadata used, the urls to the sample coverage
- bigWig files or the mean coverage bigWig file for a particular study. The
- RangedSummarizedExperiment objects can be used by different packages for
- performing differential expression analysis. Using
- http://bioconductor.org/packages/derfinder you can perform
- annotation-agnostic differential expression analyses with the data from the
- recount project as described at http://www.nature.com/nbt/journal/v35/n4/full/nbt.3838.html.
+Explore and download data from the recount project available at https://jhubiostatistics.shinyapps.io/recount/. Using the recount package you can download RangedSummarizedExperiment objects at the gene, exon or exon-exon junctions level, the raw counts, the phenotype metadata used, the urls to the sample coverage bigWig files or the mean coverage bigWig file for a particular study. The RangedSummarizedExperiment objects can be used by different packages for performing differential expression analysis. Using http://bioconductor.org/packages/derfinder you can perform annotation-agnostic differential expression analyses with the data from the recount project as described at http://www.nature.com/nbt/journal/v35/n4/full/nbt.3838.html.
}
\seealso{
Useful links:
diff --git a/man/reproduce_ranges.Rd b/man/reproduce_ranges.Rd
index 9593aec..09e8612 100644
--- a/man/reproduce_ranges.Rd
+++ b/man/reproduce_ranges.Rd
@@ -44,7 +44,6 @@ Bioconductor support forum details how to obtain the latest gene symbol
mappings: \url{https://support.bioconductor.org/p/126148/#126173}.
}
\examples{
-
\dontrun{
## Reproduce gene level information
genes <- reproduce_ranges()
diff --git a/tests/testthat/test-data.R b/tests/testthat/test-data.R
index 7e17cd2..2bab781 100644
--- a/tests/testthat/test-data.R
+++ b/tests/testthat/test-data.R
@@ -155,7 +155,6 @@ if (.Platform$OS.type != "windows") {
)
)
})
-
}
}
@@ -212,7 +211,6 @@ if (!is.null(snap)) {
expect_equal(snap_gtex$type == "GTEx:I", TRUE)
expect_equal(snap_tcga$type == "TCGA:I", TRUE)
})
-
} else {
warning("Snaptron_query() is not working! See https://github.com/ChristopherWilks/snaptron/issues/17 for more details.")
}