Browse code

make changes for R CMD check

- add documentation for cBioPortal class
- document arguments ..., sampleListId, etc.
- remove .onLoad function (cbioportal) object

LiNk-NY authored on 13/09/2019 18:27:31
Showing 8 changed files

... ...
@@ -1,6 +1,6 @@
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 Package: cBioPortalData
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 Title: Exposes and makes available data from the cBioPortal web resources
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-Version: 0.99.61
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+Version: 0.99.62
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 Authors@R: c(person("Levi", "Waldron", email = "[email protected]",
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     role = "aut"),
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     person("Marcel", "Ramos", email = "[email protected]",
... ...
@@ -10,7 +10,6 @@ Description: The cBioPortalData package takes compressed resources
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     object with Bioconductor classes.
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 Depends: R (>= 3.5.0),
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     AnVIL,
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-    methods,
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     MultiAssayExperiment
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 Remotes:
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     Bioconductor/AnVIL_rapiclient,
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@@ -31,6 +30,7 @@ Imports:
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     S4Vectors,
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     SummarizedExperiment,
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     stats,
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+    rlang,
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     tidyr,
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     TCGAutils,
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     utils
... ...
@@ -52,4 +52,3 @@ Collate:
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     'utils.R'
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     'loadStudy.R'
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     'studyDownload.R'
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-    'zzz.R'
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@@ -4,7 +4,6 @@ export(allSamples)
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 export(cBioPortal)
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 export(cBioPortalData)
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 export(cbioCache)
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-export(cbioportal)
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 export(clinicalData)
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 export(downloadStudy)
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 export(genePanelMolecular)
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@@ -52,6 +51,7 @@ importFrom(TCGAutils,findGRangesCols)
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 importFrom(TCGAutils,generateMap)
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 importFrom(methods,as)
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 importFrom(methods,is)
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+importFrom(methods,new)
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 importFrom(readr,read_tsv)
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 importFrom(readr,type_convert)
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 importFrom(stats,na.omit)
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@@ -1,7 +1,9 @@
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+utils::globalVariables(c("clinicalAttributeId", "value", "sampleId"))
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+
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 .invoke_fun <- function(api, name, ...) {
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     if (!is(api, "cBioPortal"))
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         stop("Provide a 'cBioPortal' class API object")
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-    ops <- names(operations(api))
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+    ops <- names(AnVIL::operations(api))
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     if (!name %in% ops)
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         stop("<internal> operation name not found in API")
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     do.call(`$`, list(api, name))(...)
... ...
@@ -17,9 +19,21 @@
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     .bind_content(.invoke_fun(api, name, ...))
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 }
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-#' @export
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-cbioportal <- NULL
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-
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+#' @name cBioPortal-class
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+#' 
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+#' @title A class for representing the cBioPortal API
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+#' 
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+#' @description The cBioPortal class is a product of the cBioPortal API that
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+#'     inherits from the `Service` class
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+#' 
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+#' @importFrom methods new
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+#' 
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+#' @seealso AnVIL::Service
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+#' 
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+#' @examples 
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+#' 
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+#' cbio <- cBioPortal()
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+#' 
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 #' @export
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 .cBioPortal <- setClass("cBioPortal", contains = "Service")
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... ...
@@ -142,6 +156,9 @@ clinicalData <- function(cbio, studyId) {
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 #' @section Molecular Profiles:
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 #'      * molecularProfiles - Produce a molecular profiles dataset for a given
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 #'      study identifier
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+#'  
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+#' @param projection character(default: "SUMMARY") Specify the projection
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+#'   type for data retrieval for details see API documentation
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 #'
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 #' @inheritParams cBioPortal
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 #'
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@@ -204,7 +221,7 @@ molecularSlice <- function(cbio, molecularProfileId,
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 #'
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 #' @export
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 searchOps <- function(cbio, keyword) {
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-    grep(keyword, names(operations(cbio)), value = TRUE, ignore.case = TRUE)
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+    grep(keyword, names(AnVIL::operations(cbio)), value = TRUE, ignore.case = TRUE)
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 }
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 #' @name cBioPortal
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@@ -212,6 +229,8 @@ searchOps <- function(cbio, keyword) {
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 #' @section API Metadata:
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 #'     * geneTable - Get a table of all genes by 'entrezGeneId' or
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 #'     'hugoGeneSymbol'
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+#'     
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+#' @param ... Additional arguments to lower level API functions
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 #'
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 #' @export
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 geneTable <- function(cbio, ...) {
... ...
@@ -247,7 +266,7 @@ samplesInSampleLists <- function(cbio, sampleListIds) {
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     if (missing(sampleListIds))
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         stop("Provide valid 'sampleListIds' from 'sampleLists()'")
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-    sampleListIds <- setNames(sampleListIds, sampleListIds)
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+    sampleListIds <- stats::setNames(sampleListIds, sampleListIds)
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     meta <- structure(vector("list", length(sampleListIds)),
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         .Names = sampleListIds)
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     res <- lapply(sampleListIds, function(x) {
... ...
@@ -330,6 +349,9 @@ getGenePanel <- function(cbio, genePanelId) {
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 #' @section Gene Panels:
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 #'     * genePanelMolecular - get gene panel data for a paricular
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 #'     `molecularProfileId` and `sampleListId` combination
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+#' 
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+#' @param sampleListId character(1) A sample list identifier as obtained from
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+#'     `sampleLists()``
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 #'
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 #' @export
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 genePanelMolecular <-
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@@ -364,7 +386,7 @@ genePanelMolecular <-
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 getGenePanelMolecular <-
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     function(cbio, molecularProfileIds, sampleIds)
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 {
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-    if (missing(molecularProfileId))
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+    if (missing(molecularProfileIds))
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         stop("Provide valid 'molecularProfileIds' from 'molecularProfiles()'")
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     if (missing(sampleIds))
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         stop(paste0("Provide valid 'sampleIds' from 'samplesInSampleLists()'",
... ...
@@ -467,7 +489,8 @@ getDataByGenePanel <-
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         molecularProfileIds <-
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             molecularProfiles(cbio, studyId)[["molecularProfileId"]]
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-    molecularProfileIds <- setNames(molecularProfileIds, molecularProfileIds)
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+    molecularProfileIds <- stats::setNames(molecularProfileIds,
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+        molecularProfileIds)
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     expers <- lapply(molecularProfileIds, function(molprof) {
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         moldata <- getDataByGenePanel(cbio, by = by,
... ...
@@ -489,11 +512,17 @@ getDataByGenePanel <-
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 #' data.
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 #'
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 #' @inheritParams cBioPortal
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+#' 
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+#' @param idConvert function(default: `identity()`) A function to process identifiers for matching
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+#'     patients to samples
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 #'
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 #' @examples
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 #'
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 #' cb <- cBioPortal()
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-#' cBioPortalData(cb, by = "hugoGeneSymbol")
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+#' cBioPortalData(cb, by = "hugoGeneSymbol", studyId = "acc_tcga",
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+#'     genePanelId = "IMPACT341",
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+#'     molecularProfileIds = c("acc_tcga_rppa", "acc_tcga_linear_CNA")
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+#' )
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 #'
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 #' @export
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 cBioPortalData <-
... ...
@@ -1,3 +1,5 @@
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+utils::globalVariables("element")
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+
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 .biocExtract <- function(object, names.field) {
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     hasRanged <- RTCGAToolbox:::.hasRangeNames(object)
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     build <- RTCGAToolbox:::.getBuild(object)
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@@ -149,7 +151,7 @@ endpoint_map <- data.frame(
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 .barg <- function(type) {
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     switch(type,
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-        studyId = expr(list(keyword = element)),
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+        studyId = rlang::expr(list(keyword = element)),
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         NULL
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     )
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 }
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deleted file mode 100644
... ...
@@ -1,5 +0,0 @@
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-.onLoad <-
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-    function(...)
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-{
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-    cbioportal <<- cBioPortal()
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-}
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new file mode 100644
... ...
@@ -0,0 +1,19 @@
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+% Generated by roxygen2: do not edit by hand
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+% Please edit documentation in R/cBioPortal.R
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+\docType{class}
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+\name{cBioPortal-class}
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+\alias{cBioPortal-class}
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+\alias{.cBioPortal}
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+\title{A class for representing the cBioPortal API}
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+\description{
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+The cBioPortal class is a product of the cBioPortal API that
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+    inherits from the `Service` class
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+}
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+\examples{
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+
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+cbio <- cBioPortal()
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+
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+}
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+\seealso{
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+AnVIL::Service
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+}
... ...
@@ -62,6 +62,9 @@ getDataByGenePanel(cbio, studyId, genePanelId, by = c("entrezGeneId",
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 \item{studyId}{character(1) Indicates the "studyId" as taken from
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 `getStudies`}
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+\item{projection}{character(default: "SUMMARY") Specify the projection
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+type for data retrieval for details see API documentation}
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+
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 \item{molecularProfileId}{character(1) Indicates a molecular profile ID}
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 \item{entrezGeneIds}{numeric() A vector indicating entrez gene IDs}
... ...
@@ -71,12 +74,17 @@ getDataByGenePanel(cbio, studyId, genePanelId, by = c("entrezGeneId",
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 \item{keyword}{character(1) Keyword or pattern for searching through
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 available operations}
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+\item{...}{Additional arguments to lower level API functions}
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+
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 \item{sampleListIds}{character() A vector of 'sampleListId' as obtained from
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 `sampleLists`}
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 \item{genePanelId}{character(1) Identifies the gene panel, as obtained
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 from the `genePanels` function}
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+\item{sampleListId}{character(1) A sample list identifier as obtained from
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+`sampleLists()``}
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+
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 \item{molecularProfileIds}{character() A vector of molecular profile IDs}
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 \item{by}{character(1) Whether to use 'entrezGeneId' or 'hugoGeneSymbol'
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@@ -19,8 +19,14 @@ from the `genePanels` function}
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 \item{molecularProfileIds}{character() A vector of molecular profile IDs}
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+\item{sampleListId}{character(1) A sample list identifier as obtained from
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+`sampleLists()``}
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+
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 \item{by}{character(1) Whether to use 'entrezGeneId' or 'hugoGeneSymbol'
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 as row metadata}
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+
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+\item{idConvert}{function(default: `identity()`) A function to process identifiers for matching
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+patients to samples}
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 }
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 \description{
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 Obtain a `MultiAssayExperiment` object for a particular gene panel,
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@@ -31,6 +37,9 @@ data.
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 \examples{
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 cb <- cBioPortal()
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-cBioPortalData(cb, by = "hugoGeneSymbol")
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+cBioPortalData(cb, by = "hugoGeneSymbol", studyId = "acc_tcga",
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+    genePanelId = "IMPACT341",
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+    molecularProfileIds = c("acc_tcga_rppa", "acc_tcga_linear_CNA")
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+)
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 }