v1.11.9 -- update docs

* Ran `usethis::use_roxygen_md()` + `roxygen2md::roxygen2md()` + `devtools::document()`
* Fixed the roxygen tag for an internal function

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: recount
 Title: Explore and download data from the recount project
-Version: 1.11.8
-Date: 2019-07-01
+Version: 1.11.9
+Date: 2019-08-27
 Authors@R: c(person("Leonardo", "Collado-Torres", role = c("aut", "cre"),
     email = "[email protected]", comment = c(ORCID = "0000-0003-2140-308X")),
     person("Abhinav", "Nellore", role = "ctb",
@@ -71,3 +71,4 @@ BugReports: https://support.bioconductor.org/t/recount/
 biocViews: Coverage, DifferentialExpression, GeneExpression, RNASeq, Sequencing,
     Software, DataImport, ImmunoOncology
 RoxygenNote: 6.1.1
+Roxygen: list(markdown = TRUE)

R/abstract_search.R

@@ -5,21 +5,21 @@
 #' package.
 #'
 #' @param query A character vector with the text to search for via
-#' \link[base]{grep} in the abstract info available at \link{recount_abstract}.
+#' [grep][base::grep] in the abstract info available at [recount_abstract].
 #' @param id_only Whether to only return the project id or to return summary
 #' information for the project(s) that match the query.
-#' @param ... Additional arguments passed to \link[base]{grep}.
+#' @param ... Additional arguments passed to [grep][base::grep].
 #'
-#' @return If \code{id_only = TRUE} it returns a character vector with the
-#' project SRA ids (accession numbers). If \code{id_only = FALSE} it returns a
-#' subset of \link{recount_abstract} for the abstracts that contained the query.
+#' @return If `id_only = TRUE` it returns a character vector with the
+#' project SRA ids (accession numbers). If `id_only = FALSE` it returns a
+#' subset of [recount_abstract] for the abstracts that contained the query.
 #'
 #' @details Both the query and the abstracts are searched in lower case.
 #'
 #' For a more powerful search use the recount project website at
-#' \url{https://jhubiostatistics.shinyapps.io/recount/}.
+#' <https://jhubiostatistics.shinyapps.io/recount/>.
 #'
-#' @seealso \link{browse_study}, \link{recount_abstract}
+#' @seealso [browse_study], [recount_abstract]
 #'
 #' @author Leonardo Collado-Torres
 #' @export

R/add_metadata.R

@@ -1,42 +1,42 @@
 #' Add additional curated metadata to a recount rse object
 #'
 #' This function appends sample metadata information to a
-#' \link[SummarizedExperiment]{RangedSummarizedExperiment-class} from the
+#' [RangedSummarizedExperiment-class][SummarizedExperiment::RangedSummarizedExperiment-class] from the
 #' recount2 project. The sample metadata comes from curated efforts
 #' independent from the original recount2 project. Currently the only
 #' information comes from the recount_brain project described in more detail
-#' at \url{http://lieberinstitute.github.io/recount-brain/}.
+#' at <http://lieberinstitute.github.io/recount-brain/>.
 #'
 #'
-#' @param rse A \link[SummarizedExperiment]{RangedSummarizedExperiment-class}
-#' object as downloaded with \link{download_study}. If this argument is
+#' @param rse A [RangedSummarizedExperiment-class][SummarizedExperiment::RangedSummarizedExperiment-class]
+#' object as downloaded with [download_study]. If this argument is
 #' not specified, the function will return the raw metadata table.
 #' @param source A valid source name. The only supported options at this
-#' moment are \code{recount_brain_v1} and \code{recount_brain_v2}.
-#' @param is_tcga Set to \code{TRUE} only when \code{rse} is from TCGA.
-#' Otherwise set to \code{FALSE} (default).
-#' @param verbose If \code{TRUE} it will print a message of where the
+#' moment are `recount_brain_v1` and `recount_brain_v2`.
+#' @param is_tcga Set to `TRUE` only when `rse` is from TCGA.
+#' Otherwise set to `FALSE` (default).
+#' @param verbose If `TRUE` it will print a message of where the
 #' predictions file is being downloaded to.
 #'
-#' @return A \link[SummarizedExperiment]{RangedSummarizedExperiment-class}
-#' object with the sample metadata columns appended to the \code{colData()}
+#' @return A [RangedSummarizedExperiment-class][SummarizedExperiment::RangedSummarizedExperiment-class]
+#' object with the sample metadata columns appended to the `colData()`
 #' slot.
 #'
 #' @details
-#' For \code{source = "recount_brain_v1"} and
-#' \code{source = "recount_brain_v2"}, the metadata columns are
-#' described at \url{http://lieberinstitute.github.io/recount-brain/}.
-#' Alternatively, you can explore \code{recount_brain_v2} interactively at
-#' \url{https://jhubiostatistics.shinyapps.io/recount-brain/}.
+#' For `source = "recount_brain_v1"` and
+#' `source = "recount_brain_v2"`, the metadata columns are
+#' described at <http://lieberinstitute.github.io/recount-brain/>.
+#' Alternatively, you can explore `recount_brain_v2` interactively at
+#' <https://jhubiostatistics.shinyapps.io/recount-brain/>.
 #'
 #' If you use the recount_brain data please cite the Razmara et al.
-#' bioRxiv, 2019 \url{https://www.biorxiv.org/content/10.1101/618025v1}.
+#' bioRxiv, 2019 <https://www.biorxiv.org/content/10.1101/618025v1>.
 #' A bib file is available via citation('recount')[5].
 #'
 #'
 #' @references
 #' Razmara et al, bioRxiv, 2019.
-#' \url{https://www.biorxiv.org/content/10.1101/618025v1}
+#' <https://www.biorxiv.org/content/10.1101/618025v1>
 #'
 #' @author Leonardo Collado-Torres
 #' @export

R/add_predictions.R

@@ -3,24 +3,24 @@
 #' Shannon Ellis et al (2017) predicted phenotypes based on expression data for
 #' the samples in the recount2 project. Using this function you can add the
 #' predictions to a
-#' \link[SummarizedExperiment]{RangedSummarizedExperiment-class} object
-#' to the \code{colData()} slot.
+#' [RangedSummarizedExperiment-class][SummarizedExperiment::RangedSummarizedExperiment-class] object
+#' to the `colData()` slot.
 #'
-#' @param rse A \link[SummarizedExperiment]{RangedSummarizedExperiment-class}
-#' object as downloaded with \link{download_study}. If this argument is
+#' @param rse A [RangedSummarizedExperiment-class][SummarizedExperiment::RangedSummarizedExperiment-class]
+#' object as downloaded with [download_study]. If this argument is
 #' not specified, the function will return the full predictions table.
-#' @param is_tcga Set to \code{TRUE} only when \code{rse} is from TCGA.
-#' Otherwise set to \code{FALSE} (default).
+#' @param is_tcga Set to `TRUE` only when `rse` is from TCGA.
+#' Otherwise set to `FALSE` (default).
 #' @param version The version number for the predicted phenotypes data. It has
 #' to match one of the available numbers at
-#' \url{https://github.com/leekgroup/recount-website/blob/master/predictions/}.
+#' <https://github.com/leekgroup/recount-website/blob/master/predictions/>.
 #' Feel free to check if there is a newer version than the default. The version
 #' used is printed as part of the file name.
-#' @param verbose If \code{TRUE} it will print a message of where the
+#' @param verbose If `TRUE` it will print a message of where the
 #' predictions file is being downloaded to.
 #'
-#' @return A \link[SummarizedExperiment]{RangedSummarizedExperiment-class}
-#' object with the prediction columns appended to the \code{colData()} slot.
+#' @return A [RangedSummarizedExperiment-class][SummarizedExperiment::RangedSummarizedExperiment-class]
+#' object with the prediction columns appended to the `colData()` slot.
 #' The predicted phenotypes are:
 #' \describe{
 #' \item{sex }{ male or female,}
@@ -31,8 +31,8 @@
 #' For each of the predicted phenotypes there are several columns as described
 #' next:
 #' \describe{
-#' \item{reported_phenotype }{ \code{NA} when not available,}
-#' \item{predicted_phenotype }{ \code{NA} when we did not predict, "Unassigned"
+#' \item{reported_phenotype }{ `NA` when not available,}
+#' \item{predicted_phenotype }{ `NA` when we did not predict, "Unassigned"
 #' when prediction was ambiguous,}
 #' \item{accuracy_phenotype }{ accuracy is assigned per dataset based on
 #' comparison to samples for which we had reported phenotype information so

R/all_metadata.R

@@ -3,12 +3,12 @@
 #' Download the metadata from all the projects. This can be useful for finding
 #' samples of interests across all projects.
 #'
-#' @param subset Either \code{sra},  \code{gtex} or \code{tcga}. Specifies
+#' @param subset Either `sra`,  `gtex` or `tcga`. Specifies
 #' which metadata file to download.
-#' @param verbose If \code{TRUE} it will print a message of where the file is
+#' @param verbose If `TRUE` it will print a message of where the file is
 #' being downloaded to.
 #'
-#' @return A \link[S4Vectors]{DataFrame-class} object with the phenotype
+#' @return A [DataFrame-class][S4Vectors::DataFrame-class] object with the phenotype
 #' metadata.
 #'
 #' @author Leonardo Collado-Torres
@@ -20,17 +20,17 @@
 #'
 #' metadata <- all_metadata()
 #'
-#' @details Note that for \code{subset = 'gtex'}, there are more variables than
+#' @details Note that for `subset = 'gtex'`, there are more variables than
 #' the ones we have for 'sra'. This information corresponds to file
 #' GTEx_Data_V6_Annotations_SampleAttributesDS.txt available at
-#' \url{http://www.gtexportal.org/home/datasets}. There you can find the
+#' <http://www.gtexportal.org/home/datasets>. There you can find the
 #' information describing these variables.
 #'
 #' For TCGA we acquired metadata information from 3 different sources:
 #' - GDC: via a json query
 #' - CGC: via json queries and a custom script to merge the tables
 #' - TCGAbiolinks: we used to to parse GDC's XML files
-#' For more information, check \url{https://github.com/leekgroup/recount-website/tree/master/metadata/tcga_prep}.
+#' For more information, check <https://github.com/leekgroup/recount-website/tree/master/metadata/tcga_prep>.
 #'
 
 all_metadata <- function(subset = 'sra', verbose = TRUE) {

R/browse_study.R

@@ -9,7 +9,7 @@
 #'
 #' @author Leonardo Collado-Torres
 #' @export
-#' @seealso \link{abstract_search}
+#' @seealso [abstract_search]
 #'
 #' @importFrom utils browseURL
 #'

R/coverage_matrix.R

@@ -1,46 +1,46 @@
 #' Given a set of regions for a chromosome, compute the coverage matrix for a
 #' given SRA study.
 #'
-#' Given a set of genomic regions as created by \link{expressed_regions}, this
+#' Given a set of genomic regions as created by [expressed_regions], this
 #' function computes the coverage matrix for a library size of 40 million 100 bp
 #' reads for a given SRA study.
 #'
 #' @inheritParams expressed_regions
-#' @param regions A \link[GenomicRanges]{GRanges-class} object with regions
-#' for \code{chr} for which to calculate the coverage matrix.
+#' @param regions A [GRanges-class][GenomicRanges::GRanges-class] object with regions
+#' for `chr` for which to calculate the coverage matrix.
 #' @param chunksize A single integer vector defining the chunksize to use for
 #' computing the coverage matrix. Regions will be split into different chunks
 #' which can be useful when using a parallel instance as defined by 
-#' \code{bpparam}.
-#' @param bpparam A \link[BiocParallel]{BiocParallelParam-class} instance which
+#' `bpparam`.
+#' @param bpparam A [BiocParallelParam-class][BiocParallel::BiocParallelParam-class] instance which
 #' will be used to calculate the coverage matrix in parallel. By default, 
-#' \link[BiocParallel]{SerialParam-class} will be used.
-#' @param verboseLoad If \code{TRUE} basic status updates for loading the data
+#' [SerialParam-class][BiocParallel::SerialParam-class] will be used.
+#' @param verboseLoad If `TRUE` basic status updates for loading the data
 #' will be printed.
-#' @param scale If \code{TRUE}, the coverage counts will be scaled to read 
-#' counts based on a library size of 40 million reads. Set \code{scale} to 
-#' \code{FALSE} if you want the raw coverage counts. The scaling method is by
-#' AUC, as in the default option of \link{scale_counts}.
-#' @param round If \code{TRUE}, the counts are rounded to integers. Set to 
-#' \code{TRUE} if you want to match the defaults of \link{scale_counts}.
+#' @param scale If `TRUE`, the coverage counts will be scaled to read 
+#' counts based on a library size of 40 million reads. Set `scale` to 
+#' `FALSE` if you want the raw coverage counts. The scaling method is by
+#' AUC, as in the default option of [scale_counts].
+#' @param round If `TRUE`, the counts are rounded to integers. Set to 
+#' `TRUE` if you want to match the defaults of [scale_counts].
 #' 
 #'
-#' @return A \link[SummarizedExperiment]{RangedSummarizedExperiment-class}
+#' @return A [RangedSummarizedExperiment-class][SummarizedExperiment::RangedSummarizedExperiment-class]
 #' object with the counts stored in the assays slot. 
 #'
-#' @details When using \code{outdir = NULL} the information will be accessed
+#' @details When using `outdir = NULL` the information will be accessed
 #' from the web on the fly. If you encounter internet access problems, it might
-#' be best to first download the BigWig files using \link{download_study}. This
+#' be best to first download the BigWig files using [download_study]. This
 #' might be the best option if you are accessing all chromosomes for a given
-#' project and/or are thinking of using different sets of \code{regions} (for
-#' example, from different cutoffs applied to \link{expressed_regions}).
-#' Alternatively check the \code{SciServer} section on the vignette to see
+#' project and/or are thinking of using different sets of `regions` (for
+#' example, from different cutoffs applied to [expressed_regions]).
+#' Alternatively check the `SciServer` section on the vignette to see
 #' how to access all the recount data via a R Jupyter Notebook.
 #'
-#' If you have \code{bwtool} installed, you can use
-#' \url{https://github.com/LieberInstitute/recount.bwtool} for faster results.
-#' Note that you will need to run \link{scale_counts} after running
-#' \code{coverage_matrix_bwtool()}.
+#' If you have `bwtool` installed, you can use
+#' <https://github.com/LieberInstitute/recount.bwtool> for faster results.
+#' Note that you will need to run [scale_counts] after running
+#' `coverage_matrix_bwtool()`.
 #'
 #' @author Leonardo Collado-Torres
 #' @export
@@ -49,8 +49,8 @@
 #' @import derfinder GenomicRanges RCurl BiocParallel
 #' SummarizedExperiment S4Vectors
 #'
-#' @seealso \link{download_study}, \link[derfinder]{findRegions},
-#' \link[derfinder]{railMatrix}
+#' @seealso [download_study], [findRegions][derfinder::findRegions],
+#' [railMatrix][derfinder::railMatrix]
 #'
 #' @examples
 #'

R/download_retry.R

@@ -1,23 +1,23 @@
 #' Retry multiple times to download a file
 #'
 #' This function is based on the Bioconductor guidelines for querying data from
-#' the web at \url{http://bioconductor.org/developers/how-to/web-query/}. It
-#' will run \link[downloader]{download} a set of \code{N.TRIES} times before
+#' the web at <http://bioconductor.org/developers/how-to/web-query/>. It
+#' will run [download][downloader::download] a set of `N.TRIES` times before
 #' giving up. We implemented this function to reduce the number of Bioconductor
 #' build errors due to the occassional errors from our data hosting server.
 #'
-#' @param url The URL to download. Passed to \link[downloader]{download}.
+#' @param url The URL to download. Passed to [download][downloader::download].
 #' @param destfile The destination file. Defaults to the base name of the URL.
-#' Passed to \link[downloader]{download}.
-#' @param mode Mode for writing the file. The default \code{wb} is used for
-#' binary files. This value is passed to \link[downloader]{download} which
-#' passes it to \link[utils]{download.file}.
+#' Passed to [download][downloader::download].
+#' @param mode Mode for writing the file. The default `wb` is used for
+#' binary files. This value is passed to [download][downloader::download] which
+#' passes it to [download.file][utils::download.file].
 #' @param N.TRIES The number of download attempts before giving up; default: 3.
 #' Should be an integer of length one with a value greater than 0.
-#' @param ... Additional arguments passed to \link[downloader]{download}.
+#' @param ... Additional arguments passed to [download][downloader::download].
 #'
 #' @return An invisible integer code as specified in
-#' \link[utils]{download.file}.
+#' [download.file][utils::download.file].
 #' @export
 #'
 #' @examples