From cfcbc0bec3062d3bcc5586c0ef2601496bf33ebc Mon Sep 17 00:00:00 2001
From: Fontrodona Nicolas <nicolas.fontrodona@ens-lyon.fr>
Date: Tue, 26 Sep 2023 10:08:56 +0200
Subject: [PATCH] R/load_matrix.R: fix batch effect column handling
---
R/load_matrix.R | 8 +++++---
1 file changed, 5 insertions(+), 3 deletions(-)
diff --git a/R/load_matrix.R b/R/load_matrix.R
index 2487c61..9681ee6 100644
--- a/R/load_matrix.R
+++ b/R/load_matrix.R
@@ -49,7 +49,9 @@ load_matrix <- function(design_table, path, my_formula) {
for (my_col in cn[3:length(cn)]) {
sample_table[[my_col]] <- as.factor(sample_table[[my_col]])
}
- sample_table <- sample_table[, c("sampleName", "fileName", "condition")]
+ tmp_cn <- c("sampleName", "fileName", "condition")
+ tmp_cn <- unique(c(tmp_cn, cn[3:length(cn)]))
+ sample_table <- sample_table[, tmp_cn]
sample_table$condition <- as.factor(sample_table$condition)
dds_input <- DESeq2::DESeqDataSetFromHTSeqCount(
sampleTable = as.data.frame(sample_table),
@@ -57,10 +59,10 @@ load_matrix <- function(design_table, path, my_formula) {
design = as.formula(my_formula)
)
dds <- DESeq2::DESeq(dds_input)
- if (length(cn) <= 3) {
+ if (length(tmp_cn) <= 3) {
ac <- ""
} else {
- ac <- cn[4:length(cn)]
+ ac <- tmp_cn[4:length(tmp_cn)]
}
res <- list(dds = dds, acol = ac)
return(res)
--
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