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# Copyright (C) 2014 Mohammad H. Ferdosi
#
# HSPhase is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
# HSPhase program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http:#www.gnu.org/licenses/>.
pedigreeNaming <- function(inferredPedigree, realPedigree)
{
inferredPedigree <- inferredPedigree[inferredPedigree[,1]%in%realPedigree[,1],]
realPedigree <- realPedigree[realPedigree[,1]%in%inferredPedigree[,1],]
realPedigree <- realPedigree[, 1:2]
colnames(realPedigree) <- colnames(inferredPedigree) <- c("id","group")
realPedigree$group <- as.character(realPedigree$group)
inferredPedigree$group <- as.character(inferredPedigree$group)
mergedPartition <- merge(realPedigree,inferredPedigree,by="id")
mergedPartition <- mergedPartition[order(mergedPartition[,2]),]
simfun<-function(x) {x}
opedigree <- aggregate(mergedPartition,by = list(mergedPartition$group.y),function(x)x)
index <- tapply(mergedPartition[,2],mergedPartition[,3],function(x)sort(table(as.character(x)),decreasing = T)[1],simplify = F)
frqReal <- table(unlist(lapply(index,names)))
morethan1 <- names(frqReal[frqReal>1])
for(i in 1:length(index))
{
if(all(morethan1!=names(index[[i]]) ))
inferredPedigree[inferredPedigree[,2] == names(index[i]),2] <- names(index[[i]])
else
{
ind <- which(unlist(lapply(index,names)) == names(index[[i]]))
sireName <- unlist(strsplit(names(sort(unlist(index[ind]),decreasing = T)[1]),split = "[.].*"))
inferredPedigree[inferredPedigree[,2] == sireName,2] <- names(index[[i]])
}
}
inferredPedigree
}
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