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changed README and copyright notice

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junikimm717 3 years ago
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  1. 23
      README.md
  2. 47
      src/script.def.R

23
README.md

@ -6,19 +6,26 @@ choosing (preferably halogenated compounds).
## Installation
The script has the following dependencies:
The script uses the following packages:
- latest version of the [Nontarget R Package](https://github.com/blosloos/nontarget)
(This should be installed
through the devtools package)
- [purrr](https://www.rdocumentation.org/packages/purrr/versions/0.2.5)
(It is recommended to install this package through the devtools package)
- [enviPat](https://rdocumentation.org/packages/enviPat/versions/2.2)
- [stringr](https://www.rdocumentation.org/packages/stringr/versions/1.4.0)
- [parallel](https://www.rdocumentation.org/packages/parallel/versions/3.6.2)
Before running/configuring the script, call `make` while in the `/src`
directory or copy `script.def.R` to `script.R`.
directory or simply copy `/src/script.def.R` to `/src/script.R`.
## Configuration
All configuration variables are located at the top of the script.
## Output
## Additional Notes
The script should print a list with data for all clusters that contain the
isotopes to be searched for.
In order to make the search run in linear time, as of right now, the entire
data table will be sorted before searching.
If `verbose.enable` is set to `TRUE`, files of the form `(fragment number).txt`
containing the `pattern.search` output will be printed to the directory
specified in `verbose.outputdir`, assuming the directory already exists.

47
src/script.def.R

@ -1,18 +1,34 @@
# Copyright (C) 2021-2021 Juni Christopher Kim
# This script is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This script is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with Copyright Header. If not, see <http://www.gnu.org/licenses/>.
library("nontarget")
library("enviPat")
library("stringr")
library("parallel")
# Configurations #############################################################
# file to read from
input.filename <- ""
input.filename <- " "
# separator to use (\t for tabs, "," for CSV)
input.sep <- ","
# All isotopes to check for
# All isotopes to check for in search
check_isos <- c("37Cl", "81Br")
# Minimum size of a cluster
# Minimum size of a cluster (clusters smaller than this size will not
# be accepted)
min_cluster_size <- 2
# Number of cores to be used in pattern.search evaluation
@ -21,8 +37,7 @@ use_cores <- 6
# Table name configuration
# Column name for m/z
# Column name for m/z values
columns.mz <- "mz"
# Column name for time in gc
columns.time <- "time"
@ -36,13 +51,13 @@ columns.spectra <- "Spectra_Number"
# Number of highest intensities to display in output
output.intensities <- 5
# Verbose output
verbose.enable <- TRUE
# Verbose output (dumping all output into a file)
verbose.enable <- FALSE
# output directory must already exist.
verbose.outputdir <- ""
# Script #####################################################################
# Variables/Functions ########################################################
## Defining/setting variables ################################################
@ -54,7 +69,7 @@ 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])
@ -67,7 +82,7 @@ use_cores = min(use_cores, detectCores() - 1)
minint <- rep(0, fragments)
# upper bound of indices per fragment
maxint <- rep(0, fragments)
# memoizes as to
# memoizes what clusters are usable (exist and enough data sets)
usable <- rep(FALSE, fragments)
# initialize isotopes.
@ -139,7 +154,9 @@ derive.fragment <- function(result) {
derive.iso <- function(result) {
res <- result$`Counts of isotopes`
return (res[res$"isotope" %in% check_isos, c("isotope", "group counts")])
res <-
res[res$"isotope" %in% check_isos, c("isotope", "group counts")]
return(res)
}
derive.intensity <- function(result) {
@ -162,7 +179,7 @@ derive.frame <- function(result) {
derive.average(result)
)
names(res) <-
c("Fragment_ID", "Peaks", "Intensities", "Average_time")
c("Fragment_ID", "Isotopes", "Intensities", "Average_time")
return(res)
}
@ -195,6 +212,8 @@ for (i in 1:fragments) {
usable[i] <- FALSE
}
## Run pattern.search function ##############################################
# Filter all usable fragments
use <- Filter(function(x)
usable[x], 1:fragments)
@ -205,7 +224,7 @@ results <- mclapply(use, diagnostics, mc.cores = use_cores)
results.positive <- Filter(function(x)
positive(x), results)
# print to files if verbose output requested
## Verbose output handling ##################################################
if (verbose.enable) {
if (!dir.exists(verbose.outputdir)) {
@ -232,6 +251,8 @@ if (verbose.enable) {
lapply(results.positive, verbose.dump)
}
## Data Analysis/Evaluation :################################################
result.frame <- lapply(results.positive, derive.frame)
result.fragment <- lapply(results.positive, derive.fragment)
result.iso <- lapply(results.positive, derive.iso)

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