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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/>.
.rpohhsphase <- function(genotypeMatrix, oh, forwardVectorSize = 30, excludeFP = TRUE, nsap = 3, maxRec = 15)
{
cat("id group \n",file="temp.txt")
rhsr_rc <- function(genotypeMatrix ,oh)
{
d <- as.dist(.fastdist(oh))
if(length(d)>2)
{
fit <- hclust(d, method = "ward")
groups <- cutree(fit, k = 2)
a <- which(groups==1)
b <- which(groups==2)
# print(length(a))
if(length(a)>3)
{
rec_1 <- recombinations(bmh(genotypeMatrix[a,],excludeFP = excludeFP,nsap = nsap,forwardVectorSize = forwardVectorSize))
rec_1 <- max(rec_1)
#print(paste("rec_1",rec_1))
}
else
{
rec_1 <- 9
}
print(length(b))
if(length(b)>3)
{
rec_2 <- recombinations(bmh(genotypeMatrix[b,],excludeFP = excludeFP,nsap = nsap,forwardVectorSize = forwardVectorSize))
rec_2 <- max(rec_2)
#print(paste("rec_1",rec_2))
}
else
{
rec_2 <- 9
}
if(rec_1>maxRec)
{
rhsr_rc(genotypeMatrix[a,],oh[a,a])
}
else
{
write.table(data.frame(names(a),round(abs(rnorm(1)*10^5))),"temp.txt",append = TRUE,col.names = FALSE,row.names = FALSE)
}
if(rec_2>maxRec)
{
rhsr_rc(genotypeMatrix[b,],oh[b,b])
}
else
{
write.table(data.frame(names(b),round(abs(rnorm(1)*10^6))),"temp.txt",append = TRUE,col.names = FALSE,row.names = FALSE)
}
}
else
{
if(!is.integer(oh))
{
write.table(data.frame(rownames(oh),round(abs(rnorm(1)*10^6))),"temp.txt",append = TRUE,col.names = FALSE,row.names = FALSE)
}
print(paste(class(oh),nrow(oh)))
}
}
result <- rhsr_rc(genotypeMatrix, oh)
result <-read.table("temp.txt",header = TRUE)
file.remove("temp.txt")
result
}
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