From 07fb22d64414e9ed8af2ffcfcf5c827652e82440 Mon Sep 17 00:00:00 2001
From: Fontrodona Nicolas <nicolas.fontrodona@ens-lyon.fr>
Date: Wed, 5 Jul 2023 09:53:22 +0200
Subject: [PATCH] fix load_matrix function

---
 R/load_matrix.R | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/R/load_matrix.R b/R/load_matrix.R
index 9a8dafc..2487c61 100644
--- a/R/load_matrix.R
+++ b/R/load_matrix.R
@@ -36,6 +36,7 @@ load_matrix <- function(design_table, path, my_formula) {
         path = path
     ))
     design_table$count_files <- selected_files
+    design_table <- design_table[, !names(design_table) %in% c("prefix")]
     sample_table <- dplyr::rename(design_table,
         sampleName = sample,
         fileName = count_files
@@ -49,6 +50,7 @@ load_matrix <- function(design_table, path, my_formula) {
         sample_table[[my_col]] <- as.factor(sample_table[[my_col]])
     }
     sample_table <- sample_table[, c("sampleName", "fileName", "condition")]
+    sample_table$condition <- as.factor(sample_table$condition)
     dds_input <- DESeq2::DESeqDataSetFromHTSeqCount(
         sampleTable = as.data.frame(sample_table),
         directory = ".",
-- 
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