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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/>.
rpoh <- function(genotypeMatrix, oh, forwardVectorSize = 30,excludeFP = TRUE,nsap = 3, maxRec = 15, intercept = 26.3415, coefficient = 77.3171, snpnooh, method, maxsnpnooh)
{
if(missing(method))
stop("please set the method")
METHODS <- c("recombinations", "simple","calus","manual" )
method <- pmatch(method, METHODS)
if (is.na(method))
stop("invalid pedigree reconstruction method")
if (method == -1)
stop("ambiguous pedigree reconstruction method")
if(method == 1)
{
if(forwardVectorSize == 30 && excludeFP == TRUE && nsap == 3 && maxRec == 15)
{
print("Default values will be used for identification of recombinations")
}
result <- .rpohhsphase(genotypeMatrix = genotypeMatrix,oh = oh,forwardVectorSize = forwardVectorSize,excludeFP = excludeFP,nsap = nsap, maxRec = maxRec)
}
if(method == 2)
{
if(intercept == 26.3415 && coefficient == 77.3171)
{
print("Default values will be use for caculation of maximum possible recombinations")
print(paste(snpnooh * 1000, "SNPs were used to create the oh matrix"))
}
result <- .prSimple(oh, snpnooh, intercept = intercept, coefficient = coefficient)
}
if(method == 3)
{
result <- .prCalus(oh, genotypeMatrix)
}
if(method == 4)
{
result <- .prManual(oh, maxsnpnooh)
}
result[,2] <- as.factor(result[,2])
levels(result[,2]) <- 1:length(levels(result[,2]))
result
}
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