Merge pull request #44 from bcbio/length_scaled_usage

add comment to make the user aware of options

Author: lpantano

00_params/params.R

@@ -6,6 +6,10 @@ basedir <- "./" # where to write down output files
 # This is the file used to run nf-core or compatible to that
 coldata_fn <- "/Path/to/metadata/meta.csv"
 # This file is inside star_salmon/ folder
+# Use gene_counts_length_scaled.tsv if you want to detect Differential Gene Usage from the gene counts data
+#   See more here: https://bioconductor.org/packages/devel/bioc/vignettes/tximport/inst/doc/tximport.html#Downstream_DGE_in_Bioconductor
+#   This is correct because in nf-core/rnaseq this files is created with tximport argument countsFromAbundance="lengthScaledTPM"
+#   https://github.com/nf-core/rnaseq/blob/0bb032c1e3b1e1ff0b0a72192b9118fdb5062489/modules/nf-core/tximeta/tximport/templates/tximport.r#L152
 counts_fn <- "/path/to/nf-core/output/star_salmon/salmon.merged.gene_counts.tsv"
 # This folder called "multiqc_report_data" is inside the output directory star_salmon inside multiqc folder
 multiqc_data_dir <- "/path/to/nf-core/output/multiqc/star_salmon/multiqc_report_data"

02_differential_expression/DEG.qmd

@@ -860,7 +860,9 @@ fa_gsea_list <- lapply(de_list, function(contrast) {
     input = input_entrezid, # Query for the GSEA analysis
     all_in_life = all_in_life
   ) # Annotation databases to query against
-  tb %>% filter(padj < 0.05) %>% arrange(padj) # Filter and sort the GSEA output for results with an adjust p-value less than 0.05 and return them
+  tb %>%
+    filter(padj < 0.05) %>%
+    arrange(padj) # Filter and sort the GSEA output for results with an adjust p-value less than 0.05 and return them
 })
 ```
 
@@ -981,7 +983,8 @@ fa_list <- lapply(de_list, function(contrast) {
 dt_list <- list()
 for (contrast in names(de_list)) {
   res_sig <- fa_list[[contrast]][["all"]] %>%
-    filter(padj < 0.05) %>% arrange(padj) # Filter and sort
+    filter(padj < 0.05) %>%
+    arrange(padj) # Filter and sort
   dt_list <- c(
     dt_list,
     list(h3(contrast)),