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# Copyright (C) 2013 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/>.
.hblock <- function(bmhResult, MaxBlock = 400)
{
if (!is.matrix(bmhResult))
stop("GenotypeMatrix should be a MATRIX")
expandMat <- as.double(t(bmhResult))
n <- ncol(bmhResult) * nrow(bmhResult)
fMat <- matrix(as.integer(rep(0, n)), nrow = ncol(bmhResult))
result <- .C("hblock", expandMat = as.integer(expandMat), nrow = as.integer(ncol(bmhResult)), ncol = as.integer(nrow(bmhResult)),
result = fMat, MB = as.integer(MaxBlock))$result
colnames(result) <- rownames(bmhResult)
if (!is.null(colnames(bmhResult)))
rownames(result) <- colnames(bmhResult)
t(result)
}
hbp <- function(PhasedGenotypeMatrix, PhasedSireGenotype, strand = "auto")
{
if (!is.matrix(PhasedGenotypeMatrix))
stop("PhasedGenotypeMatrix should be a MATRIX")
if (length(PhasedGenotypeMatrix[PhasedGenotypeMatrix != 0 & PhasedGenotypeMatrix != 1 &
PhasedGenotypeMatrix != 9]) > 0)
stop("PhasedGenotypeMatrix must contain only 0 and 1 or 9 for missing SNP")
if (!is.matrix(PhasedSireGenotype))
stop("PhasedSireGenotype should be a MATRIX")
if (length(PhasedSireGenotype[PhasedSireGenotype != 0 & PhasedSireGenotype != 1 & PhasedSireGenotype !=
9]) > 0)
stop("PhasedSireGenotype must contain only 0 and 1 or 9 for missing SNP")
if (ncol(PhasedGenotypeMatrix) != ncol(PhasedSireGenotype))
stop("Number of markers in sire and half-sib family must be the same")
if (nrow(PhasedSireGenotype) != 2)
stop("PhasedSireGenotype must have 2 rows")
METHODS <- c("auto", 1,2)
method <- pmatch(strand, METHODS)
if (is.na(method))
stop("invalid strand")
if (method == -1)
stop("ambiguous pedigree reconstruction method")
if (method == 1)
{
str = 0
}
else if(method == 2)
{
str = 1
}
else if(method == 3)
{
str = 2
}
expandMat <- as.numeric(t(PhasedGenotypeMatrix))
n <- ncol(PhasedGenotypeMatrix) * nrow(PhasedGenotypeMatrix)
fMat <- matrix(as.integer(rep(0, n/2)), nrow = ncol(PhasedGenotypeMatrix))
result <- .C("hbphased", expandMat = as.integer(expandMat), nrow = as.integer(nrow(PhasedGenotypeMatrix)),
ncol = as.integer(ncol(PhasedGenotypeMatrix)), result = fMat, siregenotype = as.integer(t(PhasedSireGenotype)), strand = as.integer(str))$result
if (!is.null(rownames(PhasedGenotypeMatrix)))
colnames(result) <- rownames(PhasedGenotypeMatrix)[seq(from = 1, by = 2, to = nrow(PhasedGenotypeMatrix))]
t(result)
}
phf <- function(GenotypeMatrix, blockMatrix, sirePhasedMatrix)
{
if (is.null(GenotypeMatrix) | is.null(blockMatrix) | is.null(sirePhasedMatrix))
stop("Invalid input!")
if ((!is.matrix(GenotypeMatrix)) | (!is.matrix(blockMatrix)) | (!is.matrix(sirePhasedMatrix)))
stop("All inputs should be a MATRIX")
if (length(GenotypeMatrix[GenotypeMatrix != 0 & GenotypeMatrix != 2 & GenotypeMatrix !=
1 & GenotypeMatrix != 9]) > 0)
stop("GenotypeMatrix must contain only 0,1 and 2 or 9 for missing SNPs")
if (length(blockMatrix[blockMatrix != 0 & blockMatrix != 2 & blockMatrix != 1]) > 0)
stop("blockMatrix must contain only 0,1 and 2")
if (length(sirePhasedMatrix[sirePhasedMatrix != 0 & sirePhasedMatrix != 1 & sirePhasedMatrix !=
9]) > 0)
stop("SireMatrix must contain only 0,1 and 9")
expandMat <- as.numeric(GenotypeMatrix)
n <- nrow(GenotypeMatrix) * ncol(GenotypeMatrix)
fMat <- matrix(as.integer(rep(0, n)), ncol = ncol(GenotypeMatrix))
result <- .C("phase", genotype = as.integer(GenotypeMatrix), nrow = as.integer(nrow(GenotypeMatrix)),
ncol = as.integer(ncol(GenotypeMatrix)), block = as.integer(blockMatrix), sirePhasedMatrix = as.integer(t(sirePhasedMatrix)),
result = fMat)$result
colnames(result) <- colnames(GenotypeMatrix)
result
}
.phfnoGenotype <- function(blockMatrix, sirePhasedMatrix)
{
if (length(blockMatrix[blockMatrix != 0 & blockMatrix != 2 & blockMatrix != 1]) > 0)
stop("blockMatrix must contain only 0,1 and 2")
if (length(sirePhasedMatrix[sirePhasedMatrix != 0 & sirePhasedMatrix != 1 & sirePhasedMatrix !=
9]) > 0)
stop("SireMatrix must contain only 0,1 and 9")
expandMat <- as.numeric(blockMatrix)
n <- nrow(blockMatrix) * ncol(blockMatrix)
fMat <- matrix(as.integer(rep(0, n)), ncol = ncol(blockMatrix))
.C("phaseNogenotype", nrow = as.integer(nrow(blockMatrix)),
ncol = as.integer(ncol(blockMatrix)), block = as.integer(blockMatrix), sirePhasedMatrix = as.integer(t(sirePhasedMatrix)),
result = fMat)$result
}
pm <- function(blockMatrix, method = "constant")
{
## if(missing(method))
## stop("please set the method")
METHODS <- c("constant", "relative")
method <- pmatch(method, METHODS)
if (is.na(method))
stop("invalid method")
if (method == -1)
stop("ambiguous method")
if (!is.matrix(blockMatrix))
stop("blockMatrix should be a MATRIX")
expandMat <- as.double(t(blockMatrix))
n <- ncol(blockMatrix) * nrow(blockMatrix)
fMat <- matrix(as.double(rep(0, n)), nrow = ncol(blockMatrix))
res <- .C("pm", expandMat = as.integer(expandMat), nrow = as.integer(ncol(blockMatrix)),
ncol = as.integer(nrow(blockMatrix)), method = method,result = fMat)$result
result <- t(res[-nrow(res), ])
rownames(result) <- rownames(blockMatrix)
colnames(result) <- colnames(blockMatrix)[-1]
result
}
recombinations <- function(blockMatrix)
{
if (!is.matrix(blockMatrix))
stop("The inputs must be MATRIX")
if (length(blockMatrix[blockMatrix != 0 & blockMatrix != 1 & blockMatrix != 2]) > 0)
stop("Inputs must contain only 0 and 1 or 2")
mat <- as.numeric(t(blockMatrix))
nSwitch <- integer(nrow(blockMatrix))
.C("recombinations", mat = as.integer(mat), nrow = as.integer(nrow(blockMatrix)), ncol = as.integer(ncol(blockMatrix)),
result = nSwitch)$result
}
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