R/nontargetWrap.R
In schymane/ReSOLUTION: SOLUTIONS for High ReSOLUTION Mass Spectrometry
Defines functions
nontargetWrap
Documented in
nontargetWrap
#nontarget wrapper functions
# E. Schymanski, 5/1/2017
# Documentation 3/4/2017
# data(isotopes, package="enviPat")
# data(adducts, package="enviPat")
#' Wrapper Function for Package nontarget
#'
#' @description This wrapper function runs the nontarget workflow with
#' selected default settings for positive and negative mode, creating
#' many output files to interpret the results.
#'
#' @usage nontargetWrap(peaklist_file, desc, path, pos=TRUE, inclHomol=FALSE,
#' colnums=c(1,3,5))
#'
#' @param peaklist_file File containing the peak list
#' @param desc Description - used to create file names
#' @param path Path in which to save the results files
#' @param pos Define the mode. Default \code{TRUE} indicates positive data,
#' \code{FALSE} indicates negative data.
#' @param inclHomol Indicate whether to include homologue series detection. Default \code{FALSE}.
#' If \code{TRUE}, all plus certain selected series are screened. Can be very
#' time consuming and lead to memory errors.
#' @param colnums Define the location of the mz, int and RT columns in \code{peaklist_file}.
#' The default \code{c(1,3,5)} works on enviPick output. Must be redefined for other peaklists
#' to avoid strange results!
#'
#' @return Results are saved into many output files in \code{path}
#'
#' @author Emma Schymanski (<emma.schymanski@@uni.lu>, wrapper), Martin Loos
#' (\code{\link{nontarget}}).
#'
#' @seealso \code{\link{nontarget}}.
#'
#' @export
#'
#' @examples
#'
#' #Note: this produces a lot of files, caution before trying.
#' peaklist_path <- system.file("extdata","Blind_nano_IS_toPeak750.txt",package="ReSOLUTION")
#' test_path <- paste0(getwd(),"/nontargettest")
#' dir.create(test_path)
#' nontargetWrap(peaklist_path, "BlindNanoIS_testWrap_to750", test_path, pos=TRUE, inclHomol=FALSE, colnums=c(1,3,5))
#' gc() #clear memory after.
#'
#'
nontargetWrap <- function(peaklist_file, desc, path, pos=TRUE, inclHomol=FALSE,
colnums=c(1,3,5)) {
data(isotopes, package="enviPat")
data(adducts, package="enviPat")
peaklist <- read.table(peaklist_file)
peaklist <- peaklist[,colnums]
# colnums 1,3,5 selects the correct columns from enviPick output.
# for other files, have to redefine. mz, int and RT
dir_name <- desc
full_dir_name <- paste(path,desc,sep="/")
dir.create(full_dir_name)
setwd(full_dir_name)
#remove satelite peaks
peaklist <- rm.sat(peaklist, dmz=0.3, drt=(0.1*60), intrat=0.015, spar=0.8,
corcut=-1000,plotit=TRUE)
peaklist<-peaklist[peaklist[,4],1:3]
# isotope pattern grouping
# define the isotopes
if (pos) {
iso<-make.isos(isotopes,
#take out 41K as this seems to only cause problems later
use_isotopes=c("13C","15N","34S","37Cl","81Br","13C","15N","34S","37Cl","81Br"),
use_charges=c(1,1,1,1,1,2,2,2,2,2))
#use_isotopes=c("13C","15N","34S","37Cl","81Br","41K","13C","15N","34S","37Cl","81Br","41K"),
#use_charges=c(1,1,1,1,1,1,2,2,2,2,2,2))
} else {
iso<-make.isos(isotopes,
#take out 41K as this seems to only cause problems later
use_isotopes=c("13C","15N","34S","37Cl","81Br","13C","15N","34S","37Cl","81Br"),
#use_isotopes=c("13C","15N","34S","37Cl","81Br","41K","13C","15N","34S","37Cl","81Br","41K"),
use_charges=c(-1,-1,-1,-1,-1,-2,-2,-2,-2,-2))
}
# run the grouping
pattern<-pattern.search(peaklist, iso, cutint=1000, rttol=60*c(-0.05,0.05), mztol=2,
mzfrac=0.1, ppm=TRUE, inttol=0.2,
rules=c(TRUE,TRUE,TRUE,TRUE,TRUE,TRUE,TRUE,TRUE,TRUE,TRUE,TRUE),
deter=FALSE, entry=50)
# plot the results
plot_name_ends <- c("_PlotIsotopes.pdf", "_PlotDefect_N.pdf", "_PlotDefect_C.pdf",
"_PlotDefect_S.pdf","_PlotDefect_Cl.pdf","_PlotDefect_Br.pdf","_PlotDefect_K.pdf")
plot_names <- paste(dir_name,plot_name_ends,sep="")
plot_titles <- sub(".pdf","", plot_names)
iso_plot_name <- paste(dir_name,"_PlotIsotopesAndElements.pdf",sep="")
pdf(iso_plot_name,paper="a4r")
a <- plotisotopes(pattern)
mtext(plot_titles[1], line=1)
plotdefect(pattern,elements=c("N"))
mtext(plot_titles[2], line=1)
plotdefect(pattern,elements=c("C"))
mtext(plot_titles[3], line=1)
plotdefect(pattern,elements=c("S"))
mtext(plot_titles[4], line=1)
plotdefect(pattern,elements=c("Cl"))
mtext(plot_titles[5], line=1)
plotdefect(pattern,elements=c("Br"))
mtext(plot_titles[6], line=1)
#plotdefect(pattern,elements=c("K"))
#mtext(plot_titles[7], line=1)
dev.off()
# text file output
write.table(pattern[[1]],file=paste(dir_name,"_pattern.txt", sep=""),
row.names=FALSE,quote=TRUE)#,sep=";")
write.table(a,file=paste(dir_name,"_IsotopeSummary.txt",sep=""),
row.names=FALSE,quote=FALSE)
# run grouping for the adducts and plot
if (pos) {
adduct<-adduct.search(peaklist, adducts, rttol=60*0.05, mztol=3, ppm=TRUE,
use_adducts=c("M+K","M+H","M+Na","M+NH4"), ion_mode="positive")
} else {
adduct<-adduct.search(peaklist, adducts, rttol=60*0.05, mztol=3, ppm=TRUE,
use_adducts=c("M-H","M+FA-H"), ion_mode="negative")
# adduct<-adduct.search(peaklist, adducts, rttol=60*0.05, mztol=3, ppm=TRUE,
# use_adducts=c("M-H","M+FA-H","M+Cl"), ion_mode="negative")
}
# show single pattern groups and relations
pdf(paste(dir_name,"_PlotAdducts_IsoAdd.pdf",sep=""), paper="a4r")
b <- plotadduct(adduct)
mtext(paste(dir_name,"_PlotAdduct",sep=""), line=1)
plotall(pattern,adduct)
mtext(paste(dir_name,"_PlotAllIsoAdduct",sep=""), line=1)
dev.off()
# plot for one group only - but wait until components are grouped later
#plotgroup(pattern,adduct,groupID=1,massrange=10,allmass=FALSE);
# text file output
write.table(adduct[[1]],file=paste(dir_name,"_adduct.txt", sep=""),
row.names=FALSE,quote=TRUE)#,sep=";")
write.table(b,file=paste(dir_name,"_AdductSummary.txt", sep=""),
row.names=TRUE,quote=TRUE)#,sep=";")
if (inclHomol) {
# Screen for homologous series
#RT is in seconds from enviPick, need much bigger tolerances than default (for min)
homol<-homol.search(peaklist, isotopes, elements=c("C","H","O","S","N"),use_C=TRUE,
#charge=c(-1,-2),
#charge=c(1,2), use_C=TRUE,
minmz=5, maxmz=60, minrt=0, maxrt=120,
ppm=TRUE, mztol=3.5, rttol=30, minlength=4, mzfilter=FALSE, vec_size=3E6)
#For a few distinct masses # C2H4: 28.0313 # C2H4O: 44.026215 # CH2: 14.0compI1565 # C3H6O: 58.041865
homol_select <-homol.search(peaklist, isotopes, elements=c("C","H","O","S","N"),use_C=TRUE,
#charge=c(-1),
#charge=c(1), use_C=TRUE,
minmz=5, maxmz=60, minrt=0, maxrt=120,
ppm=TRUE, mztol=3.5, rttol=30, minlength=4, vec_size=3E6,
mzfilter=c(14.01565,28.0313,44.026215,58.041865))
# for mz14 only:
homol_mz14 <-homol.search(peaklist, isotopes, elements=c("C","H","O","S","N"), use_C=TRUE,
#charge=c(-1),
# charge=c(1), use_C=TRUE,
minmz=14, maxmz=15, minrt=0, maxrt=120,
ppm=TRUE, mztol=3.5, rttol=30, minlength=4, mzfilter=14.01565, vec_size=3E6)
# for mz44 only:
homol_mz44 <-homol.search(peaklist, isotopes, elements=c("C","H","O","S","N"), use_C=TRUE,
# charge=c(1), use_C=TRUE,
#charge=c(-1),
minmz=44.026215, maxmz=45, minrt=0, maxrt=120,
ppm=TRUE, mztol=3.5, rttol=30, minlength=4, mzfilter=44.026215, vec_size=3E6)
# do the plots and writing output
pdf(paste(dir_name,"_HomologueSeries.pdf",sep=""), paper="a4r")
plothomol(homol,xlim=FALSE,ylim=FALSE,plotlegend=TRUE)
mtext(paste(dir_name,"_HomologueSeries_mz5to60_rt0to120",sep=""),line=1)
# mz 14,28,44,58
plothomol(homol_select,xlim=FALSE,ylim=FALSE,plotlegend=TRUE)
mtext(paste(dir_name,"_HomologueSeries_mz14_28_44_58_rt0to120",sep=""),line=1)
# mz 14
plothomol(homol_mz14,xlim=FALSE,ylim=FALSE,plotlegend=TRUE)
mtext(paste(dir_name,"_HomologueSeries_mz14_rt0to120",sep=""),line=1)
# mz 44
plothomol(homol_mz44,xlim=FALSE,ylim=FALSE,plotlegend=TRUE)
mtext(paste(dir_name,"_HomologueSeries_mz44_rt0to120",sep=""),line=1)
dev.off()
# all
write.table(homol[[1]],file=paste(dir_name,"_mz5to60_homol1.txt",sep=""),
row.names=FALSE,quote=TRUE)#,sep=";")
write.table(homol[[3]],file=paste(dir_name,"_mz5to60_homol3.txt",sep=""),
row.names=FALSE,quote=TRUE)#,sep=";")
# mz 14,28,44,58
write.table(homol_select[[1]],file=paste(dir_name,"_mz14_28_44_58_homol1.txt",sep=""),
row.names=FALSE,quote=TRUE)#,sep=";")
write.table(homol_select[[3]],file=paste(dir_name,"_mz14_28_44_58_homol3.txt",sep=""),
row.names=FALSE,quote=TRUE)#,sep=";")
# mz 14
write.table(homol_mz14[[1]],file=paste(dir_name,"_mz14_homol1.txt",sep=""),
row.names=FALSE,quote=TRUE)#,sep=";")
write.table(homol_mz14[[3]],file=paste(dir_name,"_mz14_homol3.txt",sep=""),
row.names=FALSE,quote=TRUE)#,sep=";")
# mz 44
write.table(homol_mz44[[1]],file=paste(dir_name,"_mz44_homol1.txt",sep=""),
row.names=FALSE,quote=TRUE)#,sep=";")
write.table(homol_mz44[[3]],file=paste(dir_name,"_mz44_homol3.txt",sep=""),
row.names=FALSE,quote=TRUE)#,sep=";")
#combining grouping results into components
comp<-combine(pattern, adduct, homol,
dont=FALSE, rules=c(TRUE,FALSE,FALSE))
} else {
comp<-combine(pattern, adduct, homol=FALSE,
dont=FALSE, rules=c(TRUE,FALSE,FALSE))
}
pdf(paste(dir_name,"_PlotIsotopes_Comp.pdf",sep=""), paper="a4r")
isoPerComp <- plotisotopes(comp)
mtext(paste(dir_name,"_PlotIsotopes_Components",sep=""),line=1)
dev.off()
write.table(comp[[1]],file=paste(dir_name,"_comp1.txt",sep=""),
row.names=FALSE,quote=TRUE)#,sep=";")
comp1 <- read.table(paste(dir_name,"_comp1.txt",sep=""), header=TRUE)
write.table(isoPerComp,file=paste(dir_name,"_IsoPerComponent.txt",sep=""),
row.names=FALSE,quote=TRUE)
# create subdir for component peaklists
subdir <- paste(full_dir_name,"/MS1_Comp_all/",sep="")
dir.create(subdir)
compID <- 0
subdir2 <- paste(full_dir_name,"/MS1_Comp_trim/",sep="")
dir.create(subdir2)
pdf(paste(dir_name,"_Plot_Individual_Components.pdf",sep=""), paper="a4r")
for(i in 1:length(comp[[1]][,1])) {
# check whether isotope or adduct group exists
ID_PatternGroup <- as.character(comp[[1]][i,2]) #stops this being a factor but allows string comparison of "-"
ID_AdductGroup <- as.character(comp[[1]][i,4])
compID <- comp[[1]][i,1]
ID_test <- length(grep("-",ID_PatternGroup)) + length(grep("-",ID_AdductGroup))
# 0 if neither are "-", 1 if one is "-", 2 if both are "-" and then we don't want peak lists
if(ID_test<2) {
a <- plotcomp(comp,compoID=compID,peakID=FALSE)
mtext(paste(dir_name,"_PlotComponent_",compID,sep=""),line=1)
#do files containing all peaks in range
filename <- paste(subdir,dir_name,"_CompPeakListAll_",compID,".txt",sep="")
#comp_peaklist <- cbind(a$'concerned peaks'[2],a$'concerned peaks'[3])
comp_peaklist <- cbind(a$'all peaks within range'[2],a$'all peaks within range'[3])
write.table(comp_peaklist,filename,row.names=FALSE,col.names=FALSE)
# do files with only the selected peaks
filename <- paste(subdir2,dir_name,"_CompPeakList_",compID,".txt",sep="")
#comp_peaklist <- cbind(a$'concerned peaks'[2],a$'concerned peaks'[3])
comp_peaklist <- cbind(a$a[2],a$a[3])
write.table(comp_peaklist,filename,row.names=FALSE,col.names=FALSE)
}
}
dev.off()
#return()
}
# nontargetWrap.csv.FIA <- function(peaklist_file, desc, path, pos=TRUE, inclHomol=FALSE,
# remSat=TRUE) {
# peaklist <- read.csv(peaklist_file)
# # This assumes peaklist as csv has mz, int and RT in correct order
# #peaklist <- peaklist[,c(1,3,5)]
# dir_name <- desc
# full_dir_name <- paste(path,desc,sep="/")
# dir.create(full_dir_name)
# setwd(full_dir_name)
#
# #remove satelite peaks
# if (remSat) {
# peaklist <- rm.sat(peaklist, dmz=0.3, drt=(0.1*60), intrat=0.015, spar=0.8,
# corcut=-1000,plotit=TRUE)
# peaklist<-peaklist[peaklist[,4],1:3]
# }
#
# # isotope pattern grouping
# # define the isotopes
# if (pos) {
# iso<-make.isos(isotopes,
# #take out 41K as this seems to only cause problems later
# use_isotopes=c("13C","15N","34S","37Cl","81Br","13C","15N","34S","37Cl","81Br"),
# use_charges=c(1,1,1,1,1,2,2,2,2,2))
# #use_isotopes=c("13C","15N","34S","37Cl","81Br","41K","13C","15N","34S","37Cl","81Br","41K"),
# #use_charges=c(1,1,1,1,1,1,2,2,2,2,2,2))
# #use_charges=c(-1,-1,-1,-1,-1,-1,-2,-2,-2,-2,-2,-2)
# } else {
# iso<-make.isos(isotopes,
# #take out 41K as this seems to only cause problems later
# use_isotopes=c("13C","15N","34S","37Cl","81Br","13C","15N","34S","37Cl","81Br"),
# #use_charges=c(1,1,1,1,1,2,2,2,2,2)
# #use_isotopes=c("13C","15N","34S","37Cl","81Br","41K","13C","15N","34S","37Cl","81Br","41K"),
# #use_charges=c(1,1,1,1,1,1,2,2,2,2,2,2)
# use_charges=c(-1,-1,-1,-1,-1,-2,-2,-2,-2,-2))
#
# }
# # run the grouping
#
# # pattern<-pattern.search(peaklist, iso, cutint=1000, rttol=60*c(-0.05,0.05), mztol=2,
# # mzfrac=0.1, ppm=TRUE, inttol=0.2,
# # rules=c(TRUE,TRUE,TRUE,TRUE,TRUE,TRUE,TRUE,TRUE,TRUE,TRUE,TRUE),
# # deter=FALSE, entry=50)
# # try some new params for FIA / TOF.
# # First try: kept cutint at 1000, mztol down to 1 from 2, inttol to 0.01 from 0.2
# pattern<-pattern.search(peaklist, iso, cutint=1000, rttol=60*c(-0.05,0.05), mztol=1,
# mzfrac=0.1, ppm=TRUE, inttol=0.01,
# rules=c(TRUE,TRUE,TRUE,TRUE,TRUE,TRUE,TRUE,TRUE,TRUE,TRUE,TRUE),
# deter=FALSE, entry=50)
# # plot the results
# plot_name_ends <- c("_PlotIsotopes.pdf", "_PlotDefect_N.pdf", "_PlotDefect_C.pdf",
# "_PlotDefect_S.pdf","_PlotDefect_Cl.pdf","_PlotDefect_Br.pdf","_PlotDefect_K.pdf")
# plot_names <- paste(dir_name,plot_name_ends,sep="")
# plot_titles <- sub(".pdf","", plot_names)
# iso_plot_name <- paste(dir_name,"_PlotIsotopesAndElements.pdf",sep="")
# pdf(iso_plot_name,paper="a4r")
# a <- plotisotopes(pattern)
# mtext(plot_titles[1], line=1)
# plotdefect(pattern,elements=c("N"))
# mtext(plot_titles[2], line=1)
# plotdefect(pattern,elements=c("C"))
# mtext(plot_titles[3], line=1)
# plotdefect(pattern,elements=c("S"))
# mtext(plot_titles[4], line=1)
# plotdefect(pattern,elements=c("Cl"))
# mtext(plot_titles[5], line=1)
# plotdefect(pattern,elements=c("Br"))
# mtext(plot_titles[6], line=1)
# #plotdefect(pattern,elements=c("K"))
# #mtext(plot_titles[7], line=1)
# dev.off()
#
# # text file output
# write.table(pattern[[1]],file=paste(dir_name,"_pattern.txt", sep=""),
# row.names=FALSE,quote=TRUE)#,sep=";")
# write.table(a,file=paste(dir_name,"_IsotopeSummary.txt",sep=""),
# row.names=FALSE,quote=FALSE)
#
# # run grouping for the adducts and plot
# if (pos) {
# adduct<-adduct.search(peaklist, adducts, rttol=60*0.05, mztol=3, ppm=TRUE,
# use_adducts=c("M+K","M+H","M+Na","M+NH4"), ion_mode="positive")
# } else {
# adduct<-adduct.search(peaklist, adducts, rttol=60*0.05, mztol=3, ppm=TRUE,
# use_adducts=c("M-H","M+FA-H"), ion_mode="negative")
# # adduct<-adduct.search(peaklist, adducts, rttol=60*0.05, mztol=3, ppm=TRUE,
# # use_adducts=c("M-H","M+FA-H","M+Cl"), ion_mode="negative")
# }
#
# # show single pattern groups and relations
# pdf(paste(dir_name,"_PlotAdducts_IsoAdd.pdf",sep=""), paper="a4r")
# b <- plotadduct(adduct)
# mtext(paste(dir_name,"_PlotAdduct",sep=""), line=1)
# plotall(pattern,adduct)
# mtext(paste(dir_name,"_PlotAllIsoAdduct",sep=""), line=1)
# dev.off()
# # plot for one group only - but wait until components are grouped later
# #plotgroup(pattern,adduct,groupID=1,massrange=10,allmass=FALSE);
# # text file output
# write.table(adduct[[1]],file=paste(dir_name,"_adduct.txt", sep=""),
# row.names=FALSE,quote=TRUE)#,sep=";")
# write.table(b,file=paste(dir_name,"_AdductSummary.txt", sep=""),
# row.names=TRUE,quote=TRUE)#,sep=";")
#
# if (inclHomol) {
# # Screen for homologous series
# #RT is in seconds from enviPick, need much bigger tolerances than default (for min)
# homol<-homol.search(peaklist, isotopes, elements=c("C","H","O","S","N"),use_C=TRUE,
# #charge=c(-1,-2),
# #charge=c(1,2), use_C=TRUE,
# minmz=5, maxmz=60, minrt=0, maxrt=120,
# ppm=TRUE, mztol=3.5, rttol=30, minlength=4, mzfilter=FALSE, vec_size=3E6)
# #For a few distinct masses # C2H4: 28.0313 # C2H4O: 44.026215 # CH2: 14.0compI1565 # C3H6O: 58.041865
# homol_select <-homol.search(peaklist, isotopes, elements=c("C","H","O","S","N"),use_C=TRUE,
# #charge=c(-1),
# #charge=c(1), use_C=TRUE,
# minmz=5, maxmz=60, minrt=0, maxrt=120,
# ppm=TRUE, mztol=3.5, rttol=30, minlength=4, vec_size=3E6,
# mzfilter=c(14.01565,28.0313,44.026215,58.041865))
# # for mz14 only:
# homol_mz14 <-homol.search(peaklist, isotopes, elements=c("C","H","O","S","N"), use_C=TRUE,
# #charge=c(-1),
# # charge=c(1), use_C=TRUE,
# minmz=14, maxmz=15, minrt=0, maxrt=120,
# ppm=TRUE, mztol=3.5, rttol=30, minlength=4, mzfilter=14.01565, vec_size=3E6)
# # for mz44 only:
# homol_mz44 <-homol.search(peaklist, isotopes, elements=c("C","H","O","S","N"), use_C=TRUE,
# # charge=c(1), use_C=TRUE,
# #charge=c(-1),
# minmz=44.026215, maxmz=45, minrt=0, maxrt=120,
# ppm=TRUE, mztol=3.5, rttol=30, minlength=4, mzfilter=44.026215, vec_size=3E6)
#
# # do the plots and writing output
# pdf(paste(dir_name,"_HomologueSeries.pdf",sep=""), paper="a4r")
# plothomol(homol,xlim=FALSE,ylim=FALSE,plotlegend=TRUE)
# mtext(paste(dir_name,"_HomologueSeries_mz5to60_rt0to120",sep=""),line=1)
# # mz 14,28,44,58
# plothomol(homol_select,xlim=FALSE,ylim=FALSE,plotlegend=TRUE)
# mtext(paste(dir_name,"_HomologueSeries_mz14_28_44_58_rt0to120",sep=""),line=1)
# # mz 14
# plothomol(homol_mz14,xlim=FALSE,ylim=FALSE,plotlegend=TRUE)
# mtext(paste(dir_name,"_HomologueSeries_mz14_rt0to120",sep=""),line=1)
# # mz 44
# plothomol(homol_mz44,xlim=FALSE,ylim=FALSE,plotlegend=TRUE)
# mtext(paste(dir_name,"_HomologueSeries_mz44_rt0to120",sep=""),line=1)
# dev.off()
#
# # all
# write.table(homol[[1]],file=paste(dir_name,"_mz5to60_homol1.txt",sep=""),
# row.names=FALSE,quote=TRUE)#,sep=";")
# write.table(homol[[3]],file=paste(dir_name,"_mz5to60_homol3.txt",sep=""),
# row.names=FALSE,quote=TRUE)#,sep=";")
# # mz 14,28,44,58
# write.table(homol_select[[1]],file=paste(dir_name,"_mz14_28_44_58_homol1.txt",sep=""),
# row.names=FALSE,quote=TRUE)#,sep=";")
# write.table(homol_select[[3]],file=paste(dir_name,"_mz14_28_44_58_homol3.txt",sep=""),
# row.names=FALSE,quote=TRUE)#,sep=";")
# # mz 14
# write.table(homol_mz14[[1]],file=paste(dir_name,"_mz14_homol1.txt",sep=""),
# row.names=FALSE,quote=TRUE)#,sep=";")
# write.table(homol_mz14[[3]],file=paste(dir_name,"_mz14_homol3.txt",sep=""),
# row.names=FALSE,quote=TRUE)#,sep=";")
# # mz 44
# write.table(homol_mz44[[1]],file=paste(dir_name,"_mz44_homol1.txt",sep=""),
# row.names=FALSE,quote=TRUE)#,sep=";")
# write.table(homol_mz44[[3]],file=paste(dir_name,"_mz44_homol3.txt",sep=""),
# row.names=FALSE,quote=TRUE)#,sep=";")
#
#
#
# #combining grouping results into components
# comp<-combine(pattern, adduct, homol,
# dont=FALSE, rules=c(TRUE,FALSE,FALSE))
# } else {
# comp<-combine(pattern, adduct, homol=FALSE,
# dont=FALSE, rules=c(TRUE,FALSE,FALSE))
# }
#
# pdf(paste(dir_name,"_PlotIsotopes_Comp.pdf",sep=""), paper="a4r")
# isoPerComp <- plotisotopes(comp)
# mtext(paste(dir_name,"_PlotIsotopes_Components",sep=""),line=1)
# dev.off()
#
# write.table(comp[[1]],file=paste(dir_name,"_comp1.txt",sep=""),
# row.names=FALSE,quote=TRUE)#,sep=";")
# comp1 <- read.table(paste(dir_name,"_comp1.txt",sep=""), header=TRUE)
# write.table(isoPerComp,file=paste(dir_name,"_IsoPerComponent.txt",sep=""),
# row.names=FALSE,quote=TRUE)
#
# # create subdir for component peaklists
# subdir <- paste(full_dir_name,"/MS1_Comp_all/",sep="")
# dir.create(subdir)
# compID <- 0
# subdir2 <- paste(full_dir_name,"/MS1_Comp_trim/",sep="")
# dir.create(subdir2)
#
# pdf(paste(dir_name,"_Plot_Individual_Components.pdf",sep=""), paper="a4r")
# for(i in 1:length(comp[[1]][,1])) {
# # check whether isotope or adduct group exists
# ID_PatternGroup <- as.character(comp[[1]][i,2]) #stops this being a factor but allows string comparison of "-"
# ID_AdductGroup <- as.character(comp[[1]][i,4])
# compID <- comp[[1]][i,1]
# ID_test <- length(grep("-",ID_PatternGroup)) + length(grep("-",ID_AdductGroup))
# # 0 if neither are "-", 1 if one is "-", 2 if both are "-" and then we don't want peak lists
# if(ID_test<2) {
# a <- plotcomp(comp,compoID=compID,peakID=FALSE)
# mtext(paste(dir_name,"_PlotComponent_",compID,sep=""),line=1)
# #do files containing all peaks in range
# filename <- paste(subdir,dir_name,"_CompPeakListAll_",compID,".txt",sep="")
# #comp_peaklist <- cbind(a$'concerned peaks'[2],a$'concerned peaks'[3])
# comp_peaklist <- cbind(a$'all peaks within range'[2],a$'all peaks within range'[3])
# write.table(comp_peaklist,filename,row.names=FALSE,col.names=FALSE)
# # do files with only the selected peaks
# filename <- paste(subdir2,dir_name,"_CompPeakList_",compID,".txt",sep="")
# #comp_peaklist <- cbind(a$'concerned peaks'[2],a$'concerned peaks'[3])
# comp_peaklist <- cbind(a$a[2],a$a[3])
# write.table(comp_peaklist,filename,row.names=FALSE,col.names=FALSE)
#
# }
# }
# dev.off()
# #return()
# }
schymane/ReSOLUTION documentation built on May 22, 2021, 3:41 a.m.
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Defines functions nontargetWrap
Documented in nontargetWrap
#nontarget wrapper functions
# E. Schymanski, 5/1/2017
# Documentation 3/4/2017
# data(isotopes, package="enviPat")
# data(adducts, package="enviPat")
#' Wrapper Function for Package nontarget
#'
#' @description This wrapper function runs the nontarget workflow with
#' selected default settings for positive and negative mode, creating
#' many output files to interpret the results.
#'
#' @usage nontargetWrap(peaklist_file, desc, path, pos=TRUE, inclHomol=FALSE,
#' colnums=c(1,3,5))
#'
#' @param peaklist_file File containing the peak list
#' @param desc Description - used to create file names
#' @param path Path in which to save the results files
#' @param pos Define the mode. Default \code{TRUE} indicates positive data,
#' \code{FALSE} indicates negative data.
#' @param inclHomol Indicate whether to include homologue series detection. Default \code{FALSE}.
#' If \code{TRUE}, all plus certain selected series are screened. Can be very
#' time consuming and lead to memory errors.
#' @param colnums Define the location of the mz, int and RT columns in \code{peaklist_file}.
#' The default \code{c(1,3,5)} works on enviPick output. Must be redefined for other peaklists
#' to avoid strange results!
#'
#' @return Results are saved into many output files in \code{path}
#'
#' @author Emma Schymanski (<emma.schymanski@@uni.lu>, wrapper), Martin Loos
#' (\code{\link{nontarget}}).
#'
#' @seealso \code{\link{nontarget}}.
#'
#' @export
#'
#' @examples
#'
#' #Note: this produces a lot of files, caution before trying.
#' peaklist_path <- system.file("extdata","Blind_nano_IS_toPeak750.txt",package="ReSOLUTION")
#' test_path <- paste0(getwd(),"/nontargettest")
#' dir.create(test_path)
#' nontargetWrap(peaklist_path, "BlindNanoIS_testWrap_to750", test_path, pos=TRUE, inclHomol=FALSE, colnums=c(1,3,5))
#' gc() #clear memory after.
#'
#'
nontargetWrap <- function(peaklist_file, desc, path, pos=TRUE, inclHomol=FALSE,
colnums=c(1,3,5)) {
data(isotopes, package="enviPat")
data(adducts, package="enviPat")
peaklist <- read.table(peaklist_file)
peaklist <- peaklist[,colnums]
# colnums 1,3,5 selects the correct columns from enviPick output.
# for other files, have to redefine. mz, int and RT
dir_name <- desc
full_dir_name <- paste(path,desc,sep="/")
dir.create(full_dir_name)
setwd(full_dir_name)
#remove satelite peaks
peaklist <- rm.sat(peaklist, dmz=0.3, drt=(0.1*60), intrat=0.015, spar=0.8,
corcut=-1000,plotit=TRUE)
peaklist<-peaklist[peaklist[,4],1:3]
# isotope pattern grouping
# define the isotopes
if (pos) {
iso<-make.isos(isotopes,
#take out 41K as this seems to only cause problems later
use_isotopes=c("13C","15N","34S","37Cl","81Br","13C","15N","34S","37Cl","81Br"),
use_charges=c(1,1,1,1,1,2,2,2,2,2))
#use_isotopes=c("13C","15N","34S","37Cl","81Br","41K","13C","15N","34S","37Cl","81Br","41K"),
#use_charges=c(1,1,1,1,1,1,2,2,2,2,2,2))
} else {
iso<-make.isos(isotopes,
#take out 41K as this seems to only cause problems later
use_isotopes=c("13C","15N","34S","37Cl","81Br","13C","15N","34S","37Cl","81Br"),
#use_isotopes=c("13C","15N","34S","37Cl","81Br","41K","13C","15N","34S","37Cl","81Br","41K"),
use_charges=c(-1,-1,-1,-1,-1,-2,-2,-2,-2,-2))
}
# run the grouping
pattern<-pattern.search(peaklist, iso, cutint=1000, rttol=60*c(-0.05,0.05), mztol=2,
mzfrac=0.1, ppm=TRUE, inttol=0.2,
rules=c(TRUE,TRUE,TRUE,TRUE,TRUE,TRUE,TRUE,TRUE,TRUE,TRUE,TRUE),
deter=FALSE, entry=50)
# plot the results
plot_name_ends <- c("_PlotIsotopes.pdf", "_PlotDefect_N.pdf", "_PlotDefect_C.pdf",
"_PlotDefect_S.pdf","_PlotDefect_Cl.pdf","_PlotDefect_Br.pdf","_PlotDefect_K.pdf")
plot_names <- paste(dir_name,plot_name_ends,sep="")
plot_titles <- sub(".pdf","", plot_names)
iso_plot_name <- paste(dir_name,"_PlotIsotopesAndElements.pdf",sep="")
pdf(iso_plot_name,paper="a4r")
a <- plotisotopes(pattern)
mtext(plot_titles[1], line=1)
plotdefect(pattern,elements=c("N"))
mtext(plot_titles[2], line=1)
plotdefect(pattern,elements=c("C"))
mtext(plot_titles[3], line=1)
plotdefect(pattern,elements=c("S"))
mtext(plot_titles[4], line=1)
plotdefect(pattern,elements=c("Cl"))
mtext(plot_titles[5], line=1)
plotdefect(pattern,elements=c("Br"))
mtext(plot_titles[6], line=1)
#plotdefect(pattern,elements=c("K"))
#mtext(plot_titles[7], line=1)
dev.off()
# text file output
write.table(pattern[[1]],file=paste(dir_name,"_pattern.txt", sep=""),
row.names=FALSE,quote=TRUE)#,sep=";")
write.table(a,file=paste(dir_name,"_IsotopeSummary.txt",sep=""),
row.names=FALSE,quote=FALSE)
# run grouping for the adducts and plot
if (pos) {
adduct<-adduct.search(peaklist, adducts, rttol=60*0.05, mztol=3, ppm=TRUE,
use_adducts=c("M+K","M+H","M+Na","M+NH4"), ion_mode="positive")
} else {
adduct<-adduct.search(peaklist, adducts, rttol=60*0.05, mztol=3, ppm=TRUE,
use_adducts=c("M-H","M+FA-H"), ion_mode="negative")
# adduct<-adduct.search(peaklist, adducts, rttol=60*0.05, mztol=3, ppm=TRUE,
# use_adducts=c("M-H","M+FA-H","M+Cl"), ion_mode="negative")
}
# show single pattern groups and relations
pdf(paste(dir_name,"_PlotAdducts_IsoAdd.pdf",sep=""), paper="a4r")
b <- plotadduct(adduct)
mtext(paste(dir_name,"_PlotAdduct",sep=""), line=1)
plotall(pattern,adduct)
mtext(paste(dir_name,"_PlotAllIsoAdduct",sep=""), line=1)
dev.off()
# plot for one group only - but wait until components are grouped later
#plotgroup(pattern,adduct,groupID=1,massrange=10,allmass=FALSE);
# text file output
write.table(adduct[[1]],file=paste(dir_name,"_adduct.txt", sep=""),
row.names=FALSE,quote=TRUE)#,sep=";")
write.table(b,file=paste(dir_name,"_AdductSummary.txt", sep=""),
row.names=TRUE,quote=TRUE)#,sep=";")
if (inclHomol) {
# Screen for homologous series
#RT is in seconds from enviPick, need much bigger tolerances than default (for min)
homol<-homol.search(peaklist, isotopes, elements=c("C","H","O","S","N"),use_C=TRUE,
#charge=c(-1,-2),
#charge=c(1,2), use_C=TRUE,
minmz=5, maxmz=60, minrt=0, maxrt=120,
ppm=TRUE, mztol=3.5, rttol=30, minlength=4, mzfilter=FALSE, vec_size=3E6)
#For a few distinct masses # C2H4: 28.0313 # C2H4O: 44.026215 # CH2: 14.0compI1565 # C3H6O: 58.041865
homol_select <-homol.search(peaklist, isotopes, elements=c("C","H","O","S","N"),use_C=TRUE,
#charge=c(-1),
#charge=c(1), use_C=TRUE,
minmz=5, maxmz=60, minrt=0, maxrt=120,
ppm=TRUE, mztol=3.5, rttol=30, minlength=4, vec_size=3E6,
mzfilter=c(14.01565,28.0313,44.026215,58.041865))
# for mz14 only:
homol_mz14 <-homol.search(peaklist, isotopes, elements=c("C","H","O","S","N"), use_C=TRUE,
#charge=c(-1),
# charge=c(1), use_C=TRUE,
minmz=14, maxmz=15, minrt=0, maxrt=120,
ppm=TRUE, mztol=3.5, rttol=30, minlength=4, mzfilter=14.01565, vec_size=3E6)
# for mz44 only:
homol_mz44 <-homol.search(peaklist, isotopes, elements=c("C","H","O","S","N"), use_C=TRUE,
# charge=c(1), use_C=TRUE,
#charge=c(-1),
minmz=44.026215, maxmz=45, minrt=0, maxrt=120,
ppm=TRUE, mztol=3.5, rttol=30, minlength=4, mzfilter=44.026215, vec_size=3E6)
# do the plots and writing output
pdf(paste(dir_name,"_HomologueSeries.pdf",sep=""), paper="a4r")
plothomol(homol,xlim=FALSE,ylim=FALSE,plotlegend=TRUE)
mtext(paste(dir_name,"_HomologueSeries_mz5to60_rt0to120",sep=""),line=1)
# mz 14,28,44,58
plothomol(homol_select,xlim=FALSE,ylim=FALSE,plotlegend=TRUE)
mtext(paste(dir_name,"_HomologueSeries_mz14_28_44_58_rt0to120",sep=""),line=1)
# mz 14
plothomol(homol_mz14,xlim=FALSE,ylim=FALSE,plotlegend=TRUE)
mtext(paste(dir_name,"_HomologueSeries_mz14_rt0to120",sep=""),line=1)
# mz 44
plothomol(homol_mz44,xlim=FALSE,ylim=FALSE,plotlegend=TRUE)
mtext(paste(dir_name,"_HomologueSeries_mz44_rt0to120",sep=""),line=1)
dev.off()
# all
write.table(homol[[1]],file=paste(dir_name,"_mz5to60_homol1.txt",sep=""),
row.names=FALSE,quote=TRUE)#,sep=";")
write.table(homol[[3]],file=paste(dir_name,"_mz5to60_homol3.txt",sep=""),
row.names=FALSE,quote=TRUE)#,sep=";")
# mz 14,28,44,58
write.table(homol_select[[1]],file=paste(dir_name,"_mz14_28_44_58_homol1.txt",sep=""),
row.names=FALSE,quote=TRUE)#,sep=";")
write.table(homol_select[[3]],file=paste(dir_name,"_mz14_28_44_58_homol3.txt",sep=""),
row.names=FALSE,quote=TRUE)#,sep=";")
# mz 14
write.table(homol_mz14[[1]],file=paste(dir_name,"_mz14_homol1.txt",sep=""),
row.names=FALSE,quote=TRUE)#,sep=";")
write.table(homol_mz14[[3]],file=paste(dir_name,"_mz14_homol3.txt",sep=""),
row.names=FALSE,quote=TRUE)#,sep=";")
# mz 44
write.table(homol_mz44[[1]],file=paste(dir_name,"_mz44_homol1.txt",sep=""),
row.names=FALSE,quote=TRUE)#,sep=";")
write.table(homol_mz44[[3]],file=paste(dir_name,"_mz44_homol3.txt",sep=""),
row.names=FALSE,quote=TRUE)#,sep=";")
#combining grouping results into components
comp<-combine(pattern, adduct, homol,
dont=FALSE, rules=c(TRUE,FALSE,FALSE))
} else {
comp<-combine(pattern, adduct, homol=FALSE,
dont=FALSE, rules=c(TRUE,FALSE,FALSE))
}
pdf(paste(dir_name,"_PlotIsotopes_Comp.pdf",sep=""), paper="a4r")
isoPerComp <- plotisotopes(comp)
mtext(paste(dir_name,"_PlotIsotopes_Components",sep=""),line=1)
dev.off()
write.table(comp[[1]],file=paste(dir_name,"_comp1.txt",sep=""),
row.names=FALSE,quote=TRUE)#,sep=";")
comp1 <- read.table(paste(dir_name,"_comp1.txt",sep=""), header=TRUE)
write.table(isoPerComp,file=paste(dir_name,"_IsoPerComponent.txt",sep=""),
row.names=FALSE,quote=TRUE)
# create subdir for component peaklists
subdir <- paste(full_dir_name,"/MS1_Comp_all/",sep="")
dir.create(subdir)
compID <- 0
subdir2 <- paste(full_dir_name,"/MS1_Comp_trim/",sep="")
dir.create(subdir2)
pdf(paste(dir_name,"_Plot_Individual_Components.pdf",sep=""), paper="a4r")
for(i in 1:length(comp[[1]][,1])) {
# check whether isotope or adduct group exists
ID_PatternGroup <- as.character(comp[[1]][i,2]) #stops this being a factor but allows string comparison of "-"
ID_AdductGroup <- as.character(comp[[1]][i,4])
compID <- comp[[1]][i,1]
ID_test <- length(grep("-",ID_PatternGroup)) + length(grep("-",ID_AdductGroup))
# 0 if neither are "-", 1 if one is "-", 2 if both are "-" and then we don't want peak lists
if(ID_test<2) {
a <- plotcomp(comp,compoID=compID,peakID=FALSE)
mtext(paste(dir_name,"_PlotComponent_",compID,sep=""),line=1)
#do files containing all peaks in range
filename <- paste(subdir,dir_name,"_CompPeakListAll_",compID,".txt",sep="")
#comp_peaklist <- cbind(a$'concerned peaks'[2],a$'concerned peaks'[3])
comp_peaklist <- cbind(a$'all peaks within range'[2],a$'all peaks within range'[3])
write.table(comp_peaklist,filename,row.names=FALSE,col.names=FALSE)
# do files with only the selected peaks
filename <- paste(subdir2,dir_name,"_CompPeakList_",compID,".txt",sep="")
#comp_peaklist <- cbind(a$'concerned peaks'[2],a$'concerned peaks'[3])
comp_peaklist <- cbind(a$a[2],a$a[3])
write.table(comp_peaklist,filename,row.names=FALSE,col.names=FALSE)
}
}
dev.off()
#return()
}
# nontargetWrap.csv.FIA <- function(peaklist_file, desc, path, pos=TRUE, inclHomol=FALSE,
# remSat=TRUE) {
# peaklist <- read.csv(peaklist_file)
# # This assumes peaklist as csv has mz, int and RT in correct order
# #peaklist <- peaklist[,c(1,3,5)]
# dir_name <- desc
# full_dir_name <- paste(path,desc,sep="/")
# dir.create(full_dir_name)
# setwd(full_dir_name)
#
# #remove satelite peaks
# if (remSat) {
# peaklist <- rm.sat(peaklist, dmz=0.3, drt=(0.1*60), intrat=0.015, spar=0.8,
# corcut=-1000,plotit=TRUE)
# peaklist<-peaklist[peaklist[,4],1:3]
# }
#
# # isotope pattern grouping
# # define the isotopes
# if (pos) {
# iso<-make.isos(isotopes,
# #take out 41K as this seems to only cause problems later
# use_isotopes=c("13C","15N","34S","37Cl","81Br","13C","15N","34S","37Cl","81Br"),
# use_charges=c(1,1,1,1,1,2,2,2,2,2))
# #use_isotopes=c("13C","15N","34S","37Cl","81Br","41K","13C","15N","34S","37Cl","81Br","41K"),
# #use_charges=c(1,1,1,1,1,1,2,2,2,2,2,2))
# #use_charges=c(-1,-1,-1,-1,-1,-1,-2,-2,-2,-2,-2,-2)
# } else {
# iso<-make.isos(isotopes,
# #take out 41K as this seems to only cause problems later
# use_isotopes=c("13C","15N","34S","37Cl","81Br","13C","15N","34S","37Cl","81Br"),
# #use_charges=c(1,1,1,1,1,2,2,2,2,2)
# #use_isotopes=c("13C","15N","34S","37Cl","81Br","41K","13C","15N","34S","37Cl","81Br","41K"),
# #use_charges=c(1,1,1,1,1,1,2,2,2,2,2,2)
# use_charges=c(-1,-1,-1,-1,-1,-2,-2,-2,-2,-2))
#
# }
# # run the grouping
#
# # pattern<-pattern.search(peaklist, iso, cutint=1000, rttol=60*c(-0.05,0.05), mztol=2,
# # mzfrac=0.1, ppm=TRUE, inttol=0.2,
# # rules=c(TRUE,TRUE,TRUE,TRUE,TRUE,TRUE,TRUE,TRUE,TRUE,TRUE,TRUE),
# # deter=FALSE, entry=50)
# # try some new params for FIA / TOF.
# # First try: kept cutint at 1000, mztol down to 1 from 2, inttol to 0.01 from 0.2
# pattern<-pattern.search(peaklist, iso, cutint=1000, rttol=60*c(-0.05,0.05), mztol=1,
# mzfrac=0.1, ppm=TRUE, inttol=0.01,
# rules=c(TRUE,TRUE,TRUE,TRUE,TRUE,TRUE,TRUE,TRUE,TRUE,TRUE,TRUE),
# deter=FALSE, entry=50)
# # plot the results
# plot_name_ends <- c("_PlotIsotopes.pdf", "_PlotDefect_N.pdf", "_PlotDefect_C.pdf",
# "_PlotDefect_S.pdf","_PlotDefect_Cl.pdf","_PlotDefect_Br.pdf","_PlotDefect_K.pdf")
# plot_names <- paste(dir_name,plot_name_ends,sep="")
# plot_titles <- sub(".pdf","", plot_names)
# iso_plot_name <- paste(dir_name,"_PlotIsotopesAndElements.pdf",sep="")
# pdf(iso_plot_name,paper="a4r")
# a <- plotisotopes(pattern)
# mtext(plot_titles[1], line=1)
# plotdefect(pattern,elements=c("N"))
# mtext(plot_titles[2], line=1)
# plotdefect(pattern,elements=c("C"))
# mtext(plot_titles[3], line=1)
# plotdefect(pattern,elements=c("S"))
# mtext(plot_titles[4], line=1)
# plotdefect(pattern,elements=c("Cl"))
# mtext(plot_titles[5], line=1)
# plotdefect(pattern,elements=c("Br"))
# mtext(plot_titles[6], line=1)
# #plotdefect(pattern,elements=c("K"))
# #mtext(plot_titles[7], line=1)
# dev.off()
#
# # text file output
# write.table(pattern[[1]],file=paste(dir_name,"_pattern.txt", sep=""),
# row.names=FALSE,quote=TRUE)#,sep=";")
# write.table(a,file=paste(dir_name,"_IsotopeSummary.txt",sep=""),
# row.names=FALSE,quote=FALSE)
#
# # run grouping for the adducts and plot
# if (pos) {
# adduct<-adduct.search(peaklist, adducts, rttol=60*0.05, mztol=3, ppm=TRUE,
# use_adducts=c("M+K","M+H","M+Na","M+NH4"), ion_mode="positive")
# } else {
# adduct<-adduct.search(peaklist, adducts, rttol=60*0.05, mztol=3, ppm=TRUE,
# use_adducts=c("M-H","M+FA-H"), ion_mode="negative")
# # adduct<-adduct.search(peaklist, adducts, rttol=60*0.05, mztol=3, ppm=TRUE,
# # use_adducts=c("M-H","M+FA-H","M+Cl"), ion_mode="negative")
# }
#
# # show single pattern groups and relations
# pdf(paste(dir_name,"_PlotAdducts_IsoAdd.pdf",sep=""), paper="a4r")
# b <- plotadduct(adduct)
# mtext(paste(dir_name,"_PlotAdduct",sep=""), line=1)
# plotall(pattern,adduct)
# mtext(paste(dir_name,"_PlotAllIsoAdduct",sep=""), line=1)
# dev.off()
# # plot for one group only - but wait until components are grouped later
# #plotgroup(pattern,adduct,groupID=1,massrange=10,allmass=FALSE);
# # text file output
# write.table(adduct[[1]],file=paste(dir_name,"_adduct.txt", sep=""),
# row.names=FALSE,quote=TRUE)#,sep=";")
# write.table(b,file=paste(dir_name,"_AdductSummary.txt", sep=""),
# row.names=TRUE,quote=TRUE)#,sep=";")
#
# if (inclHomol) {
# # Screen for homologous series
# #RT is in seconds from enviPick, need much bigger tolerances than default (for min)
# homol<-homol.search(peaklist, isotopes, elements=c("C","H","O","S","N"),use_C=TRUE,
# #charge=c(-1,-2),
# #charge=c(1,2), use_C=TRUE,
# minmz=5, maxmz=60, minrt=0, maxrt=120,
# ppm=TRUE, mztol=3.5, rttol=30, minlength=4, mzfilter=FALSE, vec_size=3E6)
# #For a few distinct masses # C2H4: 28.0313 # C2H4O: 44.026215 # CH2: 14.0compI1565 # C3H6O: 58.041865
# homol_select <-homol.search(peaklist, isotopes, elements=c("C","H","O","S","N"),use_C=TRUE,
# #charge=c(-1),
# #charge=c(1), use_C=TRUE,
# minmz=5, maxmz=60, minrt=0, maxrt=120,
# ppm=TRUE, mztol=3.5, rttol=30, minlength=4, vec_size=3E6,
# mzfilter=c(14.01565,28.0313,44.026215,58.041865))
# # for mz14 only:
# homol_mz14 <-homol.search(peaklist, isotopes, elements=c("C","H","O","S","N"), use_C=TRUE,
# #charge=c(-1),
# # charge=c(1), use_C=TRUE,
# minmz=14, maxmz=15, minrt=0, maxrt=120,
# ppm=TRUE, mztol=3.5, rttol=30, minlength=4, mzfilter=14.01565, vec_size=3E6)
# # for mz44 only:
# homol_mz44 <-homol.search(peaklist, isotopes, elements=c("C","H","O","S","N"), use_C=TRUE,
# # charge=c(1), use_C=TRUE,
# #charge=c(-1),
# minmz=44.026215, maxmz=45, minrt=0, maxrt=120,
# ppm=TRUE, mztol=3.5, rttol=30, minlength=4, mzfilter=44.026215, vec_size=3E6)
#
# # do the plots and writing output
# pdf(paste(dir_name,"_HomologueSeries.pdf",sep=""), paper="a4r")
# plothomol(homol,xlim=FALSE,ylim=FALSE,plotlegend=TRUE)
# mtext(paste(dir_name,"_HomologueSeries_mz5to60_rt0to120",sep=""),line=1)
# # mz 14,28,44,58
# plothomol(homol_select,xlim=FALSE,ylim=FALSE,plotlegend=TRUE)
# mtext(paste(dir_name,"_HomologueSeries_mz14_28_44_58_rt0to120",sep=""),line=1)
# # mz 14
# plothomol(homol_mz14,xlim=FALSE,ylim=FALSE,plotlegend=TRUE)
# mtext(paste(dir_name,"_HomologueSeries_mz14_rt0to120",sep=""),line=1)
# # mz 44
# plothomol(homol_mz44,xlim=FALSE,ylim=FALSE,plotlegend=TRUE)
# mtext(paste(dir_name,"_HomologueSeries_mz44_rt0to120",sep=""),line=1)
# dev.off()
#
# # all
# write.table(homol[[1]],file=paste(dir_name,"_mz5to60_homol1.txt",sep=""),
# row.names=FALSE,quote=TRUE)#,sep=";")
# write.table(homol[[3]],file=paste(dir_name,"_mz5to60_homol3.txt",sep=""),
# row.names=FALSE,quote=TRUE)#,sep=";")
# # mz 14,28,44,58
# write.table(homol_select[[1]],file=paste(dir_name,"_mz14_28_44_58_homol1.txt",sep=""),
# row.names=FALSE,quote=TRUE)#,sep=";")
# write.table(homol_select[[3]],file=paste(dir_name,"_mz14_28_44_58_homol3.txt",sep=""),
# row.names=FALSE,quote=TRUE)#,sep=";")
# # mz 14
# write.table(homol_mz14[[1]],file=paste(dir_name,"_mz14_homol1.txt",sep=""),
# row.names=FALSE,quote=TRUE)#,sep=";")
# write.table(homol_mz14[[3]],file=paste(dir_name,"_mz14_homol3.txt",sep=""),
# row.names=FALSE,quote=TRUE)#,sep=";")
# # mz 44
# write.table(homol_mz44[[1]],file=paste(dir_name,"_mz44_homol1.txt",sep=""),
# row.names=FALSE,quote=TRUE)#,sep=";")
# write.table(homol_mz44[[3]],file=paste(dir_name,"_mz44_homol3.txt",sep=""),
# row.names=FALSE,quote=TRUE)#,sep=";")
#
#
#
# #combining grouping results into components
# comp<-combine(pattern, adduct, homol,
# dont=FALSE, rules=c(TRUE,FALSE,FALSE))
# } else {
# comp<-combine(pattern, adduct, homol=FALSE,
# dont=FALSE, rules=c(TRUE,FALSE,FALSE))
# }
#
# pdf(paste(dir_name,"_PlotIsotopes_Comp.pdf",sep=""), paper="a4r")
# isoPerComp <- plotisotopes(comp)
# mtext(paste(dir_name,"_PlotIsotopes_Components",sep=""),line=1)
# dev.off()
#
# write.table(comp[[1]],file=paste(dir_name,"_comp1.txt",sep=""),
# row.names=FALSE,quote=TRUE)#,sep=";")
# comp1 <- read.table(paste(dir_name,"_comp1.txt",sep=""), header=TRUE)
# write.table(isoPerComp,file=paste(dir_name,"_IsoPerComponent.txt",sep=""),
# row.names=FALSE,quote=TRUE)
#
# # create subdir for component peaklists
# subdir <- paste(full_dir_name,"/MS1_Comp_all/",sep="")
# dir.create(subdir)
# compID <- 0
# subdir2 <- paste(full_dir_name,"/MS1_Comp_trim/",sep="")
# dir.create(subdir2)
#
# pdf(paste(dir_name,"_Plot_Individual_Components.pdf",sep=""), paper="a4r")
# for(i in 1:length(comp[[1]][,1])) {
# # check whether isotope or adduct group exists
# ID_PatternGroup <- as.character(comp[[1]][i,2]) #stops this being a factor but allows string comparison of "-"
# ID_AdductGroup <- as.character(comp[[1]][i,4])
# compID <- comp[[1]][i,1]
# ID_test <- length(grep("-",ID_PatternGroup)) + length(grep("-",ID_AdductGroup))
# # 0 if neither are "-", 1 if one is "-", 2 if both are "-" and then we don't want peak lists
# if(ID_test<2) {
# a <- plotcomp(comp,compoID=compID,peakID=FALSE)
# mtext(paste(dir_name,"_PlotComponent_",compID,sep=""),line=1)
# #do files containing all peaks in range
# filename <- paste(subdir,dir_name,"_CompPeakListAll_",compID,".txt",sep="")
# #comp_peaklist <- cbind(a$'concerned peaks'[2],a$'concerned peaks'[3])
# comp_peaklist <- cbind(a$'all peaks within range'[2],a$'all peaks within range'[3])
# write.table(comp_peaklist,filename,row.names=FALSE,col.names=FALSE)
# # do files with only the selected peaks
# filename <- paste(subdir2,dir_name,"_CompPeakList_",compID,".txt",sep="")
# #comp_peaklist <- cbind(a$'concerned peaks'[2],a$'concerned peaks'[3])
# comp_peaklist <- cbind(a$a[2],a$a[3])
# write.table(comp_peaklist,filename,row.names=FALSE,col.names=FALSE)
#
# }
# }
# dev.off()
# #return()
# }
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