R/fastDist.R

In hsphase: Phasing, Pedigree Reconstruction, Sire Imputation and Recombination Events Identification of Half-sib Families Using SNP Data

# 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/>.

.fastdist <- function(GenotypeMatrix)
{
	n <- nrow(GenotypeMatrix) * nrow(GenotypeMatrix)
	fMat <- matrix(as.integer(rep(0, n)), nrow = nrow(GenotypeMatrix))
	expandMat <- as.numeric(t(GenotypeMatrix))
	result <- .C("fastDist", expandMat = as.integer(expandMat), nrow = as.integer(nrow(GenotypeMatrix)), 
			ncol = as.integer(ncol(GenotypeMatrix)), result = fMat)$result
	result[upper.tri(result)] <- t(result)[upper.tri(result)]
	colnames(result)=rownames(GenotypeMatrix)
	rownames(result)=rownames(GenotypeMatrix)
	result
}