From c37a610f47f0ae04f34a1d08ca4787fca40e4cf6 Mon Sep 17 00:00:00 2001 From: junikimm717 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() }