From 40bad345efcada8db890b087b892f737f0a5e3b0 Mon Sep 17 00:00:00 2001 From: sanroman-24 Date: Tue, 7 Oct 2025 08:54:57 +0200 Subject: [PATCH 1/2] Fix condition check for indices in Gibbs.subclone.density.est function --- R/DensityEstimator.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/DensityEstimator.R b/R/DensityEstimator.R index 05989ed..41293e1 100755 --- a/R/DensityEstimator.R +++ b/R/DensityEstimator.R @@ -106,7 +106,7 @@ Gibbs.subclone.density.est <- function(burden, GS.data, pngFile, density.smooth V.h.cols <- GS.data$V.h if("pi.h" %in% names(GS.data)){ - if(is.na(indices)){ + if(all(is.na(indices))){ pi.h.cols <- GS.data$pi.h }else{ pi.h.cols <- GS.data$pi.h[,,indices] From 741d4f559c46db7ba84154a0aad42eae7c4ddb3a Mon Sep 17 00:00:00 2001 From: sanroman-24 Date: Sun, 12 Oct 2025 19:45:11 +0200 Subject: [PATCH 2/2] Improve condition check for mutation sampling in writeStandardFinalOutput function --- R/DirichletProcessClustering.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/DirichletProcessClustering.R b/R/DirichletProcessClustering.R index 541c86a..c55bd30 100755 --- a/R/DirichletProcessClustering.R +++ b/R/DirichletProcessClustering.R @@ -558,7 +558,7 @@ writeStandardFinalOutput = function(clustering, dataset, most.similar.mut, outfi ######################################################################## # Check if mutation sampling has been done, if so, unpack and assign here ######################################################################## - if (!is.na(most.similar.mut) && assign_sampled_muts) { + if (!is.null(most.similar.mut) && any(!is.na(most.similar.mut)) && isTRUE(assign_sampled_muts)) { res = unsample_mutations(dataset, clustering) dataset = res$dataset clustering = res$clustering