Merge pull request #22 from Novartis/develop

Add gene-level effective lengths (closes #6)

Author: mdshw5

pisces/R/make_expression_matrix.R

@@ -239,11 +239,17 @@ Summarize <- function(txi, tx2gene, annotation, args, metadata, species) {
     message("Writing annotation data matrix...")
     write.table(as.data.frame(annotation), paste0(args[["--name"]], ".", species, 
       ".annotation.txt"), quote = FALSE, sep = "\t", row.names = F, col.names = T)
+      
+    message("Making gene-level length matrix...")  
+    as.data.frame(txi.gene$abundance) %>% tibble::rownames_to_column("gene_id") %>% 
+      left_join(annotation) %>% as.data.frame %>%
+      write.table(format(., nsmall = 3, scientific = F, trim = T), paste0(args[["--name"]], 
+      ".", species, ".length.txt"), quote = FALSE, sep = "\t", row.names = F, 
+      col.names = T)
 
-    message("Making raw TPM matrix...")
+    message("Making gene-level TPM matrix...")
     raw_df <- as.data.frame(txi.gene$abundance) %>% tibble::rownames_to_column("gene_id") %>% 
       left_join(annotation) %>% as.data.frame
-    
 
     if (!args[["--no-rescale"]]) {
       message(paste("Scaling TPM of", args[["--scale-tpm"]], "to 1e6..."))
@@ -263,6 +269,7 @@ Summarize <- function(txi, tx2gene, annotation, args, metadata, species) {
     write.table(format(normed_df, nsmall = 3, scientific = F, trim = T), paste0(args[["--name"]], 
       ".", species, ".log2fc.txt"), quote = FALSE, sep = "\t", row.names = F, 
       col.names = T)
+
 
 
     message(paste("Calculating TMM scaling factors using", args[["--scale-tpm"]],