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Verified Commit 07fb22d6 authored by nfontrod's avatar nfontrod
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fix load_matrix function

parent 3a64aea6
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...@@ -36,6 +36,7 @@ load_matrix <- function(design_table, path, my_formula) { ...@@ -36,6 +36,7 @@ load_matrix <- function(design_table, path, my_formula) {
path = path path = path
)) ))
design_table$count_files <- selected_files design_table$count_files <- selected_files
design_table <- design_table[, !names(design_table) %in% c("prefix")]
sample_table <- dplyr::rename(design_table, sample_table <- dplyr::rename(design_table,
sampleName = sample, sampleName = sample,
fileName = count_files fileName = count_files
...@@ -49,6 +50,7 @@ load_matrix <- function(design_table, path, my_formula) { ...@@ -49,6 +50,7 @@ load_matrix <- function(design_table, path, my_formula) {
sample_table[[my_col]] <- as.factor(sample_table[[my_col]]) sample_table[[my_col]] <- as.factor(sample_table[[my_col]])
} }
sample_table <- sample_table[, c("sampleName", "fileName", "condition")] sample_table <- sample_table[, c("sampleName", "fileName", "condition")]
sample_table$condition <- as.factor(sample_table$condition)
dds_input <- DESeq2::DESeqDataSetFromHTSeqCount( dds_input <- DESeq2::DESeqDataSetFromHTSeqCount(
sampleTable = as.data.frame(sample_table), sampleTable = as.data.frame(sample_table),
directory = ".", directory = ".",
......
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