From ad464123a5a964b909a7e4ee3b4d3198835186d9 Mon Sep 17 00:00:00 2001
From: igor <6363505+igordot@users.noreply.github.com>
Date: Tue, 24 May 2022 16:46:49 -0400
Subject: [PATCH] Check for state markers before diffcyt() DS test

calcMedians() throws an uninformative error if no state markers are present
---
 R/diffcyt_wrapper.R | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/R/diffcyt_wrapper.R b/R/diffcyt_wrapper.R
index fe91d10..edd956b 100644
--- a/R/diffcyt_wrapper.R
+++ b/R/diffcyt_wrapper.R
@@ -415,6 +415,9 @@ diffcyt <- function(d_input, experiment_info = NULL, marker_info = NULL,
   if (verbose) message("calculating features...")
   d_counts <- calcCounts(d_se)
   if (analysis_type == "DS") {
+    if (!("state" %in% colData(d_se)$marker_class)) {
+      stop("no 'state' markers are present in the object")
+    }
     d_medians <- calcMedians(d_se)
     d_medians_by_cluster_marker <- calcMediansByClusterMarker(d_se)
     d_medians_by_sample_marker <- calcMediansBySampleMarker(d_se)