Nothing
getPara.sAGP <- function(){
para<-NULL
para$inputdata<-'' #input data, for segment purity calculation
para$savedata<-''
para$pngdir<-''
para$purityfile<-''
para$thr.kmeans<-0.1
para$K<-12 ## constant parameter for objective function F (see details in getSegPurity)
para$BAFfilter<-10
para$thr.originsize<-500
para$is.plot<-FALSE
para$is.normalize<-TRUE
para$std.BAF<-0.025
para$std.LRR<-0.1
para$max.cn<-NULL ## maximum copy number examined. Default NULL, this number is determined by ploidy+4
para$strictness<-1.1 ## if 1, strict. larger than 1 indicating segments can have >1 AGP, due to noise
para$is.seed<-TRUE
para$res.r<-0.8 # permutation resample ratio
para$is.LRRcorrection<-FALSE
para$is.multicore<-FALSE
para$is.scale<-FALSE #When computing minimun distance from segment to canonical track, if rescale BAF, recommended F.
para$LRR_correction_del<-0.572
para$LRR_correction_amp<-0.553
para$originFile<-'Origin.Rdata'
para$sensitivity<-FALSE ## if perform sensitivity analysis
para$ss.BAF<-0.02 ## radius of random sampling region
para$ss.LRR<-0.08
para$ss.N<-10
para$ss.dir<-''
return(para)
}
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