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Update assets/RNAseq_report.Rmd
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WackerO authored Dec 3, 2024

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2 changes: 1 addition & 1 deletion assets/RNAseq_report.Rmd
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@@ -629,7 +629,7 @@ if (params$input_type %in% c("featurecounts", "smrnaseq")) {
coldata$combfactor <- metadata$combfactor
rownames(coldata) <- qbicCodes
cds <- DESeqDataSetFromTximport(txi=txi.salmon, colData =coldata, design = eval(parse(text=as.character(design[[1]]))))
# get raw counts
# get raw counts
count_table_names <- merge(x=gene_names, y=assay(cds), by.x = "Ensembl_ID", by.y="row.names")
count_table_names <- count_table_names[order(count_table_names$Ensembl_ID),]
write.table(count_table_names, paste("differential_gene_expression/gene_counts_tables/raw_gene_counts.tsv",sep=""), append = FALSE, quote = FALSE, sep = "\t",eol = "\n", na = "NA", dec = ".", row.names = F, qmethod = c("escape", "double"))

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