restoring handling of peptides

Author: vladpetyuk

R/read_FragPipe_TMT.R

@@ -54,18 +54,19 @@ read_FragPipe_TMT <- function(path = NULL, org_to_retain = NULL, use_gene_as_pro
    }
 
    # make featureNames
-   if (grepl("multi-site|peptide", basename(path_to_file))) {
-
+   if (grepl("peptide", basename(path_to_file))) {
+      df <- df %>%
+         mutate(rowname = paste(Gene, ProteinID, Peptide, sep = "|"))
+   }
+   else if (grepl("multi-site", basename(path_to_file))) {
       df <- df %>% mutate(rowname = paste(Gene,
                                           ProteinID,
                                           str_split_i(Index, "_", i = 4),
                                           Peptide,
                                           sep = "|"))
-
       df <- df %>%
          dplyr::filter(
             str_split_i(Index, "_", i = 4) == str_split_i(Index, "_", i = 5))
-
    }
    else if (grepl("single-site", basename(path_to_file))) {
       if(use_gene_as_prot_id){