From 3a5cb3a56dcbba346cf3a7146fabdacaf2473033 Mon Sep 17 00:00:00 2001 From: Mateusz Staniak Date: Fri, 21 Apr 2023 15:24:04 +0200 Subject: [PATCH] Fixed dropping missing groups from contrasts Fixed dropping missing groups from contrasts --- R/utils_group_comparison.R | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/R/utils_group_comparison.R b/R/utils_group_comparison.R index ef2d384..355cabd 100644 --- a/R/utils_group_comparison.R +++ b/R/utils_group_comparison.R @@ -417,8 +417,8 @@ fit_Group_Sub_model = function(data) { #' @return a contrast vector .makeContrastSingleTMT = function(fit, contrast, single_protein, coefs) { sub_groups = as.character(unique(single_protein$Group)) - positive = names(contrast)[contrast > 0] - negative = names(contrast)[contrast < 0] + positive = colnames(contrast)[contrast > 0] + negative = colnames(contrast)[contrast < 0] if (!(all(positive %in% sub_groups) & all(negative %in% sub_groups))) { contrast_updated = unname(contrast[, sub_groups]) @@ -471,4 +471,4 @@ fit_Group_Sub_model = function(data) { new_values = new_values * abs(1 / sum(new_values, na.rm = TRUE)) contrast[condition] = new_values contrast -} \ No newline at end of file +}