diff --git a/DESCRIPTION b/DESCRIPTION index ddb9e5e..a8fa948 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: categoryCompare2 -Version: 0.100.11 +Version: 0.100.12 Title: Meta-Analysis of High-Throughput Experiments Using Feature Annotations Author: Robert M. Flight diff --git a/NAMESPACE b/NAMESPACE index 9a11954..f3d87f7 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -59,26 +59,15 @@ exportClasses(combined_enrichment) exportClasses(hypergeom_features) exportClasses(node_assign) exportClasses(statistical_results) -exportMethods(Extract) -exportMethods(a) exportMethods(annotation_combinations) exportMethods(combine_annotations) exportMethods(combine_enrichments) -exportMethods(enrich) -exportMethods(enrichment) -exportMethods(extract) exportMethods(extract_statistics) -exportMethods(from) exportMethods(generate_annotation_graph) exportMethods(generate_table) exportMethods(get_significant_annotations) -exportMethods(object.) exportMethods(remove_edges) exportMethods(show) -exportMethods(single) -exportMethods(statistical) -exportMethods(stats) -exportMethods(table) import(methods) importFrom(base64enc,dataURI) importFrom(colorspace,desaturate) diff --git a/R/combine_enrichments.R b/R/combine_enrichments.R index a4acf80..4fde843 100644 --- a/R/combine_enrichments.R +++ b/R/combine_enrichments.R @@ -576,16 +576,6 @@ setMethod("extract_statistics", signature = list(in_results = "combined_enrichme use_names = base_enrich_names) } -#' add data to graph -#' -#' given a \code{\link{combined_enrichment}} object, add the data about the significant -#' and present annotations, their descriptions, links (if present), and all the statistics, -#' and add that data to the annotation graph object. -#' -#' @param combined_enrichment a \code{\link{combined_enrichment}} object -#' @exportMethod - - #' extract enrich stats #' #' Extract statistical table from a single enrichment object. @@ -601,3 +591,13 @@ extract_enrich_stats = function(enrichment_result) stats$description = enrichment_result@annotation@description[stats$ID] return(stats) } + + +#' add data to graph +#' +#' given a \code{\link{combined_enrichment}} object, add the data about the significant +#' and present annotations, their descriptions, links (if present), and all the statistics, +#' and add that data to the annotation graph object. +#' +#' @param combined_enrichment a \code{\link{combined_enrichment}} object +#' @exportMethod diff --git a/man/extract_enrich_stats.Rd b/man/extract_enrich_stats.Rd index 67ff8d2..5e79183 100644 --- a/man/extract_enrich_stats.Rd +++ b/man/extract_enrich_stats.Rd @@ -2,20 +2,16 @@ % Please edit documentation in R/combine_enrichments.R \name{extract_enrich_stats} \alias{extract_enrich_stats} -\title{add data to graph} +\title{extract enrich stats} \usage{ extract_enrich_stats(enrichment_result) } \arguments{ \item{enrichment_result}{the enrichment result object} - -\item{combined_enrichment}{a \code{\link{combined_enrichment}} object} } \value{ data.frame } \description{ -given a \code{\link{combined_enrichment}} object, add the data about the significant -and present annotations, their descriptions, links (if present), and all the statistics, -and add that data to the annotation graph object. +Extract statistical table from a single enrichment object. }