diff --git a/DESCRIPTION b/DESCRIPTION index 447b7d7..e246d38 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -90,6 +90,6 @@ Suggests: muscData, broom biocViews: scater, scran, SingleCellExperiment, ComplexHeatmap, muscData, ExperimentHub -Remotes: sqjin/CellChat, saezlab/OmnipathR, saezlab/decoupleR, LTLA/basilisk.utils, LTLA/basilisk -RoxygenNote: 7.2.3 +Remotes: sqjin/CellChat, saezlab/OmnipathR, saezlab/decoupleR, Bioconductor/basilisk.utils, Bioconductor/basilisk +RoxygenNote: 7.3.0 Config/testthat/edition: 3 diff --git a/R/liana_ortho.R b/R/liana_ortho.R index ff526fa..64dff0f 100644 --- a/R/liana_ortho.R +++ b/R/liana_ortho.R @@ -58,7 +58,6 @@ generate_homologs <- function(op_resource, symbols_dict <- get_homologene_dict(entities = entities, target_organism = target_organism) - # Remove any missing antities if(is.null(.missing_fun)){ @@ -254,7 +253,15 @@ recode.character2 <- function(.x, .default = NULL, .missing = NULL, .missing_fun) { + .x <- as.character(.x) + + if (length(.x) == 0) { + + return(.x) + + } + values <- rlang::list2(...) if (!all(rlang::have_name(values))) { bad <- which(!rlang::have_name(values)) + 1 @@ -399,7 +406,7 @@ get_homologene_dict <- function(entities, id_type = "genesymbol"){ # Load homology geneset - hg_gs <- homologene_download(target = !!target_organism, + hg_gs <- homologene_download(target = target_organism, source = 9606L, # always human id_type = !!id_type) %>% select(-hgroup) %>%