diff --git a/R/msigdbr-collections.R b/R/msigdbr-collections.R index b42b0fc..204ecb0 100644 --- a/R/msigdbr-collections.R +++ b/R/msigdbr-collections.R @@ -5,12 +5,8 @@ #' @param db_species Species abbreviation for the human or mouse databases (`"Hs"` or `"Mm"`). #' #' @importFrom dplyr arrange count distinct -#' @export #' -#' @examples -#' \donttest{ -#' msigdbr_collections() -#' } +#' @export msigdbr_collections <- function(db_species = "Hs") { # Check that msigdbdf is installed msigdbr_check_data() diff --git a/R/msigdbr-species.R b/R/msigdbr-species.R index 2009164..bcdeefe 100644 --- a/R/msigdbr-species.R +++ b/R/msigdbr-species.R @@ -6,9 +6,6 @@ #' @importFrom dplyr arrange distinct select #' #' @export -#' -#' @examples -#' msigdbr_species() msigdbr_species <- function() { babelgene::species() |> as_tibble() |> diff --git a/R/msigdbr.R b/R/msigdbr.R index 0cdc4b6..c29164b 100644 --- a/R/msigdbr.R +++ b/R/msigdbr.R @@ -8,7 +8,7 @@ #' Starting with release 2022.1, MSigDB incorporated a database of mouse-native gene sets and was split into human and mouse divisions ("Hs" and "Mm"). #' Each one is provided in the approved gene symbols of its respective species. #' The versioning convention of MSigDB is in the format `Year.Release.Species`. -#' The genes within each gene set may originate from a species different from the database target species, indicated by the `gs_source_species` and `db_target_species` fields. +#' The genes within each gene set may originate from a species different from the database target species as indicated by the `gs_source_species` and `db_target_species` fields. #' #' Mouse MSigDB includes gene sets curated from mouse-centric datasets and specified in native mouse gene identifiers, eliminating the need for ortholog mapping. #' @@ -27,17 +27,6 @@ #' @importFrom dplyr arrange distinct filter inner_join mutate rename select #' #' @export -#' -#' @examples -#' # get all human gene sets -#' \donttest{ -#' msigdbr(species = "Homo sapiens") -#' } -#' -#' # get mouse C2 (curated) CGP (chemical and genetic perturbations) gene sets -#' \donttest{ -#' msigdbr(species = "Mus musculus", collection = "C2", subcollection = "CGP") -#' } msigdbr <- function(species = "Homo sapiens", db_species = "HS", collection = NULL, subcollection = NULL, category = deprecated(), subcategory = deprecated()) { # Check that msigdbdf is installed msigdbr_check_data() diff --git a/man/msigdbr.Rd b/man/msigdbr.Rd index ea623b8..431d309 100644 --- a/man/msigdbr.Rd +++ b/man/msigdbr.Rd @@ -39,21 +39,10 @@ Historically, the MSigDB resource has been tailored to the analysis of human-spe Starting with release 2022.1, MSigDB incorporated a database of mouse-native gene sets and was split into human and mouse divisions ("Hs" and "Mm"). Each one is provided in the approved gene symbols of its respective species. The versioning convention of MSigDB is in the format \code{Year.Release.Species}. -The genes within each gene set may originate from a species different from the database target species, indicated by the \code{gs_source_species} and \code{db_target_species} fields. +The genes within each gene set may originate from a species different from the database target species as indicated by the \code{gs_source_species} and \code{db_target_species} fields. Mouse MSigDB includes gene sets curated from mouse-centric datasets and specified in native mouse gene identifiers, eliminating the need for ortholog mapping. } -\examples{ -# get all human gene sets -\donttest{ -msigdbr(species = "Homo sapiens") -} - -# get mouse C2 (curated) CGP (chemical and genetic perturbations) gene sets -\donttest{ -msigdbr(species = "Mus musculus", collection = "C2", subcollection = "CGP") -} -} \references{ \url{https://www.gsea-msigdb.org/gsea/msigdb/index.jsp} } diff --git a/man/msigdbr_collections.Rd b/man/msigdbr_collections.Rd index 2c197f6..9695137 100644 --- a/man/msigdbr_collections.Rd +++ b/man/msigdbr_collections.Rd @@ -15,8 +15,3 @@ A data frame of the available collections. \description{ List the collections available in the msigdbr package } -\examples{ -\donttest{ -msigdbr_collections() -} -} diff --git a/man/msigdbr_species.Rd b/man/msigdbr_species.Rd index 705d7fe..95abbc9 100644 --- a/man/msigdbr_species.Rd +++ b/man/msigdbr_species.Rd @@ -12,6 +12,3 @@ A data frame of the available species. \description{ List the species available in the msigdbr package } -\examples{ -msigdbr_species() -}