diff --git a/DESCRIPTION b/DESCRIPTION index 3bd3aa3..6a31b5a 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: isomiRs Version: 1.31.2 -Date: 2024-03-13 +Date: 2024-04-30 Type: Package Title: Analyze isomiRs and miRNAs from small RNA-seq Description: Characterization of miRNAs and isomiRs, clustering and @@ -17,11 +17,10 @@ Suggests: BiocStyle, testthat Depends: - R (>= 4.0), + R (>= 4.4), SummarizedExperiment Imports: AnnotationDbi, - assertive.sets, BiocGenerics, Biobase, broom, diff --git a/NAMESPACE b/NAMESPACE index 12e04f5..f9e69ec 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -29,7 +29,6 @@ import(GenomicRanges) import(IRanges) import(S4Vectors) import(SummarizedExperiment) -import(assertive.sets) import(cluster) import(gtools) import(methods) diff --git a/NEWS b/NEWS index 0500c85..667c102 100644 --- a/NEWS +++ b/NEWS @@ -1,6 +1,6 @@ - Changes in version 1.31.2 (Ă–mer An) +* remove `assertive.sets` * Add gitactions * Add color to PCA plot by `isoTop` function * Fix depreciated dplyr code diff --git a/R/isomiRs-package.R b/R/isomiRs-package.R index d6cae07..9064a8f 100644 --- a/R/isomiRs-package.R +++ b/R/isomiRs-package.R @@ -11,7 +11,6 @@ #' @import GGally #' @import gtools #' @import Biobase -#' @import assertive.sets #' @import cluster #' @importFrom AnnotationDbi keys mget revmap #' @importFrom reshape melt melt.array melt.data.frame melt.list diff --git a/R/targets.R b/R/targets.R index 7da8706..b51ebd2 100644 --- a/R/targets.R +++ b/R/targets.R @@ -275,7 +275,7 @@ isoNetwork <- function(mirna_rse, gene_rse, net <- res %>% separate_rows("geneID") %>% .[,c("ID", "Description", "geneID")] # browser() - if (!are_intersecting_sets(net[["geneID"]], names(gene_rse))){ + if (length(intersect(net[["geneID"]], names(gene_rse))) == 0){ message("No matching genes between enrich and gene_rse.") mapping <- .is_mapping_needed(names(gene_rse), net$geneID) message(" Converting from ", mapping[[1]], " to ", mapping[[2]])