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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/>.
pogc <- function(oh, genotypeError)
{
diag(oh) <- NA
halfsib <- apply(oh, 1, function(x) names(which(x < genotypeError)))
halfsib <- halfsib[unlist(lapply(halfsib, length)) > 2]
if (length(halfsib) > 0)
{
repeated <- lapply(halfsib, length)
pedigree <- data.frame(unlist(halfsib), rep(names(halfsib), repeated))
colnames(pedigree) <- c("offspring", "parent")
return(pedigree)
}
print("Could not find any groups!")
}
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