zinba=function(outfile=NULL,seq=NULL,align=NULL,input="none",twoBit=NULL,basecountfile=NULL,threshold=0.05,numProc=1,
refinepeaks=1,printFullOut=0,filetype="bowtie",extension=NULL,broad=FALSE, mode="peaks", interaction=TRUE, FDR=TRUE,
genome="hg"
){
if(is.null(outfile)){stop("output prefix must be specified")}
if(is.null(seq)){stop("path to mapped experimental reads must be specified")}
if(!file.exists(seq)){stop("sequencing file does not exist at the specified path, check path for errors")}
if(!file.exists(align)){stop("mappability directory does not exist at the specified path, check path for errors")}
if(!file.exists(input) & input!="none"){stop("sequencing file does not exist at the specified path, check path for errors")}
if(!file.exists(twoBit)){stop(".2bit file does not exist at the specified path, check path for errors")}
if(is.null(basecountfile) & refinepeaks==1){stop("basecount file needs to be specified for peak refinement")}
if(is.null(extension)){stop("sequencing read extension length (average length of fragment library) needs to be specified")}
#base parameters
buildwin=1
winSize=250
offset=125
cnvWinSize=100000
cnvOffset=2500
pquant=1
initmethod="count"
printFullOut=1
diff=0
pWinSize=200
method="mixture"
selectmodel=TRUE
selectchr="chr22"
selecttype="dirty"
winGap=0
#peakconfidence=1-threshold this is now done in run.zinba
#options
if(genome=="hg" || genome=="mm"){
if(broad==TRUE) winGap=5000
if(input=="none" & broad==FALSE){
selectcovs=c("gcPerc", "align_perc", "exp_cnvwin_log")
}else if(input=="none" & broad==TRUE){
selectcovs=c("gcPerc", "align_perc")
}else if(input!="none"){
selectcovs=c("input_count")
selecttype="complete"
}
if(genome=="mm") selectchr="chr19"
}else if(genome=="othersmall" || genome=="ce" ||genome=="dm"){
winSize=200
offset=40
if(broad==TRUE) winGap=2000
if(input=="none" & broad==FALSE){
selectcovs=c("gcPerc", "exp_cnvwin_log", "align_perc")
}else if(input=="none" & broad==TRUE){
selectcovs=c("gcPerc","align_perc")
}else if(input!="none"){
selectcovs=c("input_count")
selecttype="complete"
}
if(genome=="dm") selectchr="chr2L"
else if(genome=="ce") selectchr="chrI"
}else{
stop("'genome' should be either 'hg', 'mm', 'dm', 'ce', 'othersmall'")
}
if(mode=="peaks"){
run.zinba(
align=align,
numProc=numProc,
seq=seq,
input=input,
basecountfile=basecountfile,
filetype=filetype,
offset=offset,
buildwin=1,
outfile=outfile,
threshold=threshold,
twoBit=twoBit,
cnvOffset=cnvOffset,
pquant=1,
winGap=winGap,
cnvWinSize=cnvWinSize,
initmethod="count",
printFullOut=printFullOut,
winSize=winSize,
diff=0,
pWinSize=200,
extension=extension,
method="mixture",
refinepeaks=refinepeaks,
selectmodel=TRUE,
selectchr=selectchr,
selecttype=selecttype,
selectcovs=selectcovs,
FDR=FDR,
interaction=interaction #,
#peakconfidence=peakconfidence this is now deprecated
)
}else if(mode=="CNV"){
run.zinba(
align=align,
numProc=numProc,
seq=seq,
input=input,
basecountfile=basecountfile,
filetype=filetype,
offset=2500,
buildwin=1,
outfile=outfile,
threshold=0.05,
twoBit=twoBit,
cnvOffset=2500,
pquant=1,
winGap=10000,
cnvWinSize=100000,
initmethod="count",
printFullOut=1,
winSize=10000,
diff=0,
pWinSize=200,
extension=extension,
method="mixture",
refinepeaks=refinepeaks,
selectmodel=FALSE,
formula=exp_count~1,
formulaE=exp_count~1,
formulaZ=exp_count~1,
FDR=FALSE,
#peakconfidence=0.95,
interaction=interaction
)
}
}
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