Nothing
enviPickwrap <-
function( filepath.mzXML,
MSlevel=c(1),
dmzgap=15,
dmzdens=4,
ppm=TRUE,
drtgap=500,
drtsmall=20,
drtdens=250,
drtfill=10,
drttotal=200,
minpeak=4,
recurs=3,
weight=2,
SB=3,
SN=2,
minint=1E5,
maxint=1E7,
ended=2,
ion_mode=FALSE,
progbar=FALSE
){
##########################################################################
# checks & setups ########################################################
if(!is.integer(minpeak)){minpeak<-ceiling(minpeak);minpeak<-as.integer(minpeak)}
if(minpeak<=1){stop("minpeak must be >1")}
if(!is.loaded("agglom")){stop(".Call to agglom failed; aborted.")}
if(!is.loaded("indexed")){stop(".Call to indexed failed; aborted.")}
if(!is.loaded("densvec")){stop(".Call to densvec failed")}
if(!is.loaded("pickpeak")){stop(".Call to pickpeak failed!")};
if(!is.loaded("gapfill")){stop(".Call to gapfill failed!")};
if(!is.loaded("picklist")){stop(".Call to picklist failed!")};
if(!is.loaded("getEIC")){stop(".Call to getEIC failed")}
if(!is.logical(ppm)){stop("invalid ppm argument, TRUE or FALSE")}
if(!is.logical(progbar)){stop("invalid progbar argument, TRUE or FALSE")}
if(dmzdens<=0 || drtdens<=0){stop("invalid: drtdens or dmzdens <= 0")}
if(drtsmall<=0 || drtsmall<=0){stop("drt must be >0!")};
if(minint>=maxint){stop("Revise your minint & maxint settings!")}
if(ended<1){stop("Wrong ended argument!")}
if(!is.integer(recurs)){recurs<-ceiling(recurs);recurs<-as.integer(recurs)}
if(!is.integer(ended)){ended<-ceiling(ended);ended<-as.integer(ended)}
##########################################################################
if(progbar==TRUE){ prog<-winProgressBar("Peak Picking",min=0,max=5);
setWinProgressBar(prog, 1, title = "Peak Picking - reading scans", label = NULL);}
MSlist<-readMSdata(filepath.mzXML,MSlevel,progbar=FALSE,minRT=FALSE,maxRT=FALSE,minmz=FALSE,maxmz=FALSE,ion_mode=ion_mode);
if(progbar==TRUE){setWinProgressBar(prog, 2, title = "Peak Picking - Partition", label = NULL);}
MSlist<-mzagglom(MSlist,dmzgap,ppm,drtgap,minpeak,maxint,progbar=FALSE)
if(progbar==TRUE){setWinProgressBar(prog, 3, title = "Peak Picking - EIC cluster", label = NULL);}
MSlist<-mzclust(MSlist,dmzdens,ppm,drtdens,minpeak,merged=TRUE,maxint,progbar=FALSE,from=FALSE,to=FALSE)
if(progbar==TRUE){setWinProgressBar(prog, 4, title = "Peak Picking - Peaks in EICs", label = NULL);}
MSlist<-mzpick(MSlist,minpeak,drtsmall,drtfill,drttotal,recurs,weight,SB,SN,minint,maxint,
ended,progbar=FALSE,from=FALSE,to=FALSE)
if(progbar==TRUE){setWinProgressBar(prog, 5, title = "Peak Picking - done.", label = NULL);
Sys.sleep(0.5);close(prog);}
##########################################################################
return(MSlist);
}
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