'updateMeans_FinalPolish' <- function(tmp, datA, datL, germHomozyg.mBAF.thr=0.97)
{
tt = which(is.na(datA))
if (length(tt)!=0) {
datA[tt] = 1
}
tt = which((datA>1))
if (length(tt)!=0) {
datA[tt] = 1
}
for (k in 1:dim(tmp)[1]) {
if (tmp[k,GAP::.GapEnv$c_if]>tmp[k,GAP::.GapEnv$c_is]+10) {
tmp[k,GAP::.GapEnv$c_lrr] = median(datL[tmp[k,GAP::.GapEnv$c_is]:tmp[k,GAP::.GapEnv$c_if]],na.rm=TRUE)
} else {
if (tmp[k,GAP::.GapEnv$c_if]>tmp[k,GAP::.GapEnv$c_is]) {
tmp[k,GAP::.GapEnv$c_lrr] = mean(datL[tmp[k,GAP::.GapEnv$c_is]:tmp[k,GAP::.GapEnv$c_if]],na.rm=TRUE)
} else {
tmp[k,GAP::.GapEnv$c_lrr] = datL[tmp[k,GAP::.GapEnv$c_is]]
}
}
}
ad = datA
tt = which(datA>germHomozyg.mBAF.thr)
if (length(tt)!=0) {
ad[tt] = NA
}
for (k in 1:dim(tmp)[1]) {
adv = ad[tmp[k,GAP::.GapEnv$c_is]:tmp[k,GAP::.GapEnv$c_if]]
tt = which(!is.na(adv))
if (length(tt)>length(adv)/8) {
adv = adv[tt]
if (length(adv)>30) {
tmp[k,GAP::.GapEnv$c_baf] = median(adv,na.rm=TRUE)
if (tmp[k,GAP::.GapEnv$c_baf]<0.6) {
hh = hist(adv, breaks=seq(0.5,1,0.02),right=FALSE,plot=FALSE)
if ((sum(hh$counts[1:3])/sum(hh$counts)>0.7)&&((hh$counts[1]+hh$counts[2])>2*hh$counts[3]*1.2)) {
if (hh$counts[1]>hh$counts[2]) {
tmp[k,GAP::.GapEnv$c_baf] = 0.5
} else {
tmp[k,GAP::.GapEnv$c_baf] = 0.52
}
} else {
dd = density(adv,n=20)
tmp[k,GAP::.GapEnv$c_baf] = dd$x[which.max(dd$y)]
}
}
} else {
if (length(adv)>0) {
hh = hist(adv, breaks=seq(0.5,1,0.05),plot=FALSE)
tmp[k,GAP::.GapEnv$c_baf] = hh$mids[which.max(hh$counts)]
} else {
tmp[k,GAP::.GapEnv$c_baf] = NA
}
}
} else {
tt = which(is.na(adv))
adv = datA[tmp[k,GAP::.GapEnv$c_is]:tmp[k,GAP::.GapEnv$c_if]]
if (length(tt)>10) {
adv = adv[tt]
if (length(adv)>30) {
dd = density(adv,n=20)
tmp[k,GAP::.GapEnv$c_baf] = dd$x[which.max(dd$y)]
} else {
hh = hist(adv, breaks=seq(0.5,1,0.05),right=FALSE,plot=FALSE)
tmp[k,GAP::.GapEnv$c_baf] = hh$mids[which.max(hh$counts)]
}
} else {
if (length(tt)>0) {
adv = adv[tt]
hh = hist(adv, breaks=seq(0.5,1,0.1),plot=FALSE)
tmp[k,GAP::.GapEnv$c_baf] = hh$mids[which.max(hh$counts)]
} else {
tmp[k,GAP::.GapEnv$c_baf] = NA
}
}
}
}
tmp = round(tmp,4)
return(invisible(tmp))
}
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