'fitShortSubclones' <- function(tmp, Centr_CL, NETM, p_BAF, Length)
{
TMP = tmp
tt = which(TMP[,GAP::.GapEnv$c_len]>=Length)
tt1 = table(TMP[,GAP::.GapEnv$c_chr])
if (length(which(tt1==1))>0) {
tt1 = tt1[which(tt1==1)]
tt1 = as.numeric(rownames(tt1))
for (j in 1:length(tt1)) {
tt = c(tt,which(TMP[,GAP::.GapEnv$c_chr]==tt1[j]))
}
tt = as.numeric(rownames(table(tt)))
}
if (length(tt)>0) {
tMP = TMP[-tt,]
TMP = TMP[tt,]
}
TMP = UniteSEGtmp_Illum(TMP, p_BAF)
TMP = adjustTMPstableSubclone(TMP,Centr_CL,NETM,p_BAF)
TMP = UniteSEGtmp_Illum(TMP,p_BAF)
tmp[,GAP::.GapEnv$c_conf] = 0
for (k in 1:dim(TMP)[1]) {
tt = which(tmp[,GAP::.GapEnv$c_is]>=TMP[k,GAP::.GapEnv$c_is])
if (length(tt)>0) {
kk = which(tmp[tt,GAP::.GapEnv$c_if]<=TMP[k,GAP::.GapEnv$c_if])
if (length(kk)>0) {
tmp[tt[kk],GAP::.GapEnv$c_CN] = TMP[k,GAP::.GapEnv$c_CN]
tmp[tt[kk],GAP::.GapEnv$c_BA] = TMP[k,GAP::.GapEnv$c_BA]
tmp[tt[kk],GAP::.GapEnv$c_conf] = k
}
}
}
for (k in 1:dim(tMP)[1]) {
tt = which(tmp[,GAP::.GapEnv$c_ind]==tMP[k,GAP::.GapEnv$c_ind])
if (length(tt)>0) {
tmp[tt,GAP::.GapEnv$c_conf] = -k
}
}
return(invisible(tmp))
}
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