quick-fix duplicated loci for mapman

workflows/functional_mapman.R

@@ -2,12 +2,17 @@ load(file = "runs/kallisto_combined/mothertableV3.Rdata")
 
 # now we make a data.frame with the data required for Mapman loading
 # if you have more fold-changes, you can load more than one
-forMapman <- dfr[, c("locus", "log2FC")]
+forMapman <- dfr[!duplicated(dfr$locus), c("locus", "log2FC")]
+
+### TODO: the `duplicated` solution is a quick-and-dirty fix to avoid duplicated 
+### locus IDs coming from mapping on transcript level 
+### (plus Mapman accepts AT1G01040, not AT1G01040.1)
+
 head(forMapman)
 # now we export the data.frame in biologist and mapman readable format
 dir.create(path = "runs/mapman", recursive = T, showWarnings = F)
 write.table(forMapman,
-  file = "runs/mapman/forMapmanloading.txt",
+  file = "runs/_backup/mapman/forMapmanloading.txt",
   quote = F, sep = "\t", row.names = F
 )
 remove(forMapman)