diff Rscripts/filter-RIDB.R @ 0:9d5f4f5f764b

Initial commit to toolshed

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Rscripts/filter-RIDB.R	Thu Jan 16 13:10:00 2014 +0100
@@ -0,0 +1,56 @@
+##
+#
+# Removes duplicates from a RI-database
+#
+# Usage:
+#       Rscript filter-RIDB.R /path/to/retention_db.txt output_RIDB_file.txt
+#
+##
+
+# Commandline arguments
+args  <- commandArgs(TRUE)
+ridb <- args[1]
+out_file <- args[2]
+
+# Function to check duplicates
+duplicates <- function(dat) { 
+     s <- do.call("order", as.data.frame(dat)) 
+     non.dup <- !duplicated(dat[s, ]) 
+     orig.ind <- s[non.dup] 
+     first.occ <- orig.ind[cumsum(non.dup)] 
+     first.occ[non.dup] <- NA 
+     first.occ[order(s)]
+}
+
+# Load CSV file
+ridb <- read.csv(ridb,header=TRUE, sep="\t")
+## Filters on: CAS FORMULA Column type Column phase type Column name
+filter_cols <- c(1, 3, 5, 6, 7)
+cat("RIDB dimensions: ")
+print(dim(ridb))
+deleted <- NULL
+cat("Checking for duplicates...")
+dups <- duplicates(ridb[,filter_cols])
+cat("\t[DONE]\nRemoving duplicates...")
+newridb <- ridb
+newridb["min"] <- NA
+newridb["max"] <- NA
+newridb["orig.columns"] <- NA
+for (i in unique(dups)) {
+    if (!is.na(i)) {
+        rows <- which(dups == i)
+        duprows <- ridb[c(i, rows),]
+        # Replace duplicate rows with one row containing the median value
+        new_RI <- median(duprows$RI)
+        newridb$RI[i] <- median(duprows$RI)
+        newridb$min[i] <- min(duprows$RI)
+        newridb$max[i] <- max(duprows$RI)
+        newridb$orig.columns[i] <- paste(rows, collapse=",")
+        deleted <- c(deleted, rows)
+    }
+}
+cat("\t\t[DONE]\nCreating new dataset...")
+out_ridb <- newridb[-deleted,]
+cat("\t\t[DONE]\nWriting new dataset...")
+write.table(out_ridb, na='', file=out_file, quote=T, sep="\t", row.names=F)
+cat("\t\t[DONE]\n")