diff --git a/DESCRIPTION b/DESCRIPTION index 96b4ddcb..9b687cf7 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: QFeatures Title: Quantitative features for mass spectrometry data -Version: 1.13.1 +Version: 1.13.2 Authors@R: c(person("Laurent", "Gatto", email = "laurent.gatto@uclouvain.be", comment = c(ORCID = "0000-0002-1520-2268"), @@ -24,7 +24,7 @@ Imports: IRanges, SummarizedExperiment, BiocGenerics, - ProtGenerics (>= 1.27.1), + ProtGenerics (>= 1.35.1), AnnotationFilter, lazyeval, Biobase, @@ -82,4 +82,4 @@ Collate: 'utils.R' 'display.R' Roxygen: list(markdown=TRUE) -RoxygenNote: 7.2.3 +RoxygenNote: 7.3.0 diff --git a/NAMESPACE b/NAMESPACE index 0682e382..60b316c5 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -92,3 +92,4 @@ importFrom(methods,slot) importFrom(methods,validObject) importFrom(stats,heatmap) importFrom(utils,read.csv) +importMethodsFrom(ProtGenerics,filterFeatures) diff --git a/R/AllGenerics.R b/R/AllGenerics.R index 5a5c46f9..50305f2d 100644 --- a/R/AllGenerics.R +++ b/R/AllGenerics.R @@ -4,10 +4,6 @@ ##' @rdname AllGenerics NULL - -setGeneric("filterFeatures", - function(object, filter, ...) standardGeneric("filterFeatures")) - setGeneric("subsetByFeature", function(x, y, ...) standardGeneric("subsetByFeature")) diff --git a/R/QFeatures-filter.R b/R/QFeatures-filter.R index 3090b71f..47d5181a 100644 --- a/R/QFeatures-filter.R +++ b/R/QFeatures-filter.R @@ -236,6 +236,8 @@ VariableFilter <- function(field, ##' ##' @exportMethod filterFeatures ##' +##' @importMethodsFrom ProtGenerics filterFeatures +##' ##' @rdname QFeatures-filtering setMethod("filterFeatures", c("QFeatures", "AnnotationFilter"),