From c37a610f47f0ae04f34a1d08ca4787fca40e4cf6 Mon Sep 17 00:00:00 2001
From: junikimm717 <junikimm717@gmail.com>
Date: Wed, 21 Jul 2021 14:24:46 -0400
Subject: [PATCH] changed some minor mistakes

---
 src/script.def.R | 31 +++++++++++++++++--------------
 1 file changed, 17 insertions(+), 14 deletions(-)

diff --git a/src/script.def.R b/src/script.def.R
index 551e5ec..ef76a74 100644
--- a/src/script.def.R
+++ b/src/script.def.R
@@ -19,31 +19,31 @@ library("parallel")
 
 # Configurations #############################################################
 
-# file to read from
-input.filename <- " "
+# absolute path of the file that contains data.
+input.filename <- ""
 # separator to use (\t for tabs, "," for CSV)
 input.sep <- ","
 
 # All isotopes to check for in search
 check_isos <- c("37Cl", "81Br")
 
-# Minimum size of a cluster (clusters smaller than this size will not
-# be accepted)
+# Minimum size of a cluster (clusters smaller than this size will be filtered out)
 min_cluster_size <- 2
 
 # Number of cores to be used in pattern.search evaluation
-# (will be adjusted if it exceeds the true number of cores)
+# (this value will be adjusted if it exceeds the true number of cores)
 use_cores <- 6
 
 
-# Table name configuration
+# Configuration of column names
+
 # Column name for m/z values
 columns.mz <- "mz"
-# Column name for time in gc
+# Column name for time in gas chromatography
 columns.time <- "time"
 # Column name for intensities
 columns.intensity <- "Intensity"
-# Column name for fragment numbers (only numbers accepted)
+# Column name for fragment numbers (numerical values)
 columns.spectra <- "Spectra_Number"
 
 # output options
@@ -51,10 +51,13 @@ columns.spectra <- "Spectra_Number"
 # Number of highest intensities to display in output
 output.intensities <- 5
 
-# Verbose output (dumping all output into a file)
-verbose.enable <- FALSE
+# Enable Verbose output (dumping all output into a file)
+verbose.enable <- TRUE
+
+# output directory for dumping all files
 # output directory must already exist.
-verbose.outputdir <- ""
+verbose.outputdir <-
+    "/home/junikim/programming/patternmatch/data/results"
 
 
 # Variables/Functions ########################################################
@@ -69,7 +72,7 @@ if (!("13C" %in% search_isos)) {
 }
 # Read in the Table and sort by spectra ID
 table <- read.table(input.filename, header = TRUE, sep = input.sep)
-table <- table[order(table[, columns.spectra]),]
+table <- table[order(table[, columns.spectra]), ]
 
 # Organize the tables by number
 fragments <- max(table[, columns.spectra])
@@ -167,7 +170,7 @@ derive.intensity <- function(result) {
 }
 
 derive.average <- function(result) {
-    ptrn <- result$Patterns[, 2]
+    ptrn <- result$Patterns[, 3]
     return(mean(ptrn))
 }
 
@@ -189,7 +192,7 @@ verbose.dump <- function(result) {
                   paste(derive.fragment(result), ".txt",
                         sep = ""))
     sink(path)
-    dput(result)
+    write.table(result$Patterns, sep = "\t")
     sink()
 }