diff --git a/R/enrichViewNet.R b/R/enrichViewNet.R index 06d279e..c2401c7 100644 --- a/R/enrichViewNet.R +++ b/R/enrichViewNet.R @@ -328,25 +328,26 @@ NULL #' #' @aliases parentalNapaVsDMSOEnrichment #' -#' @format a \code{list} containing 2 entries: +#' @format a \code{list} created by gprofiler2 that contains the results +#' from the enrichment analysis: #' \itemize{ -#' \item{result} {a \code{data.frame} with the significantly enriched -#' terms } -#' \item{meta} {a TODO} +#' \item{\code{"result"}: a \code{data.frame} with the significantly +#' enriched terms } +#' \item{\code{"meta"}: a \code{list} with the meta-data information} #' } -#' +#' #' @return a \code{list} containing 2 entries: #' \itemize{ -#' \item{result} {a \code{data.frame} with the significantly enriched -#' terms } -#' \item{meta} {a TODO} +#' \item{\code{"result"}: a \code{data.frame} with the significantly +#' enriched terms } +#' \item{\code{"meta"}: a \code{list} with the meta-data information} #' } #' #' @seealso #' \itemize{ -#' \item{\code{\link{createNetwork}}} {for transforming functional +#' \item{\link{createNetwork}} {for transforming functional #' enrichment results from gprofiler2 into a Cytoscape network} -#' \item{\code{\link{createEnrichMap}}} {for transforming functional +#' \item{\link{createEnrichMap}} {for transforming functional #' enrichment results from gprofiler2 into an enrichment map} #' } #' @@ -375,17 +376,16 @@ NULL #' Omnibus (GEO) under the accession number GSE135352. #' #' @examples -#' -#' ## Required library -#' library(gprofiler2) #' -#' ## Loading dataset containing the results of a differentially expressed +#' ## Loading dataset containing the results of the enrichment analysis +#' ## done on a differentially expressed #' ## analysis between 2-hour treatment with 0.5 uM napabucasin and #' ## DMSO vehicle control parental MiaPaCa2 cells #' data(parentalNapaVsDMSOEnrichment) #' -#' ## TODO -#' +#' ## Create an enrichment map for the GO:CC terms +#' createEnrichMap(gostObject=parentalNapaVsDMSOEnrichment, +#' query="parental_napa_vs_DMSO", source="GO:CC") #' NULL diff --git a/man/parentalNapaVsDMSOEnrichment.Rd b/man/parentalNapaVsDMSOEnrichment.Rd index 7f2d316..006800c 100644 --- a/man/parentalNapaVsDMSOEnrichment.Rd +++ b/man/parentalNapaVsDMSOEnrichment.Rd @@ -10,11 +10,12 @@ The cells were treated for 2 hour with 0.5 uM napabucasin. The protocol to generate the RNA-seq is described in Froeling F.E.M. et al 2019.} \format{ -a \code{list} containing 2 entries: +a \code{list} created by gprofiler2 that contains the results +from the enrichment analysis: \itemize{ -\item{result} {a \code{data.frame} with the significantly enriched -terms } -\item{meta} {a TODO} + \item{\code{"result"}: a \code{data.frame} with the significantly + enriched terms } + \item{\code{"meta"}: a \code{list} with the meta-data information} } } \source{ @@ -27,9 +28,9 @@ data(parentalNapaVsDMSOEnrichment) \value{ a \code{list} containing 2 entries: \itemize{ -\item{result} {a \code{data.frame} with the significantly enriched -terms } -\item{meta} {a TODO} + \item{\code{"result"}: a \code{data.frame} with the significantly + enriched terms } + \item{\code{"meta"}: a \code{list} with the meta-data information} } } \description{ @@ -61,23 +62,22 @@ as background. } \examples{ -## Required library -library(gprofiler2) - -## Loading dataset containing the results of a differentially expressed +## Loading dataset containing the results of the enrichment analysis +## done on a differentially expressed ## analysis between 2-hour treatment with 0.5 uM napabucasin and ## DMSO vehicle control parental MiaPaCa2 cells data(parentalNapaVsDMSOEnrichment) -## TODO - +## Create an enrichment map for the GO:CC terms +createEnrichMap(gostObject=parentalNapaVsDMSOEnrichment, + query="parental_napa_vs_DMSO", source="GO:CC") } \seealso{ \itemize{ - \item{\code{\link{createNetwork}}} {for transforming functional + \item{\link{createNetwork}} {for transforming functional enrichment results from gprofiler2 into a Cytoscape network} - \item{\code{\link{createEnrichMap}}} {for transforming functional + \item{\link{createEnrichMap}} {for transforming functional enrichment results from gprofiler2 into an enrichment map} } }