R/prManual.R

# 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/>.

.prManual <- function(oh, maxsnpnooh)
{
	cat("id group \n", file = "temp.txt")
	rhsr_rc <- function(oh, maxsnpnooh = maxsnpnooh)
	{
		print("----")
		## d <- dist(oh, method = 'manhattan')
		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)
			
			
			if (length(a) > 2)
			{
				subohA <- oh[a, a]
				maxSubohA <- max(subohA[lower.tri(subohA)])
			} else
			{
				maxSubohA <- 0
			}
			
			if (length(b) > 2)
			{
				subohB <- oh[b, b]
				maxSubohB <- max(subohB[lower.tri(subohB)])
			} else
			{
				maxSubohB <- 0
			}
			
			if (maxSubohA > maxsnpnooh && length(a) > 2)
			{
				
				rhsr_rc(oh[a, a], maxsnpnooh)
			} else
			{
				
				write.table(data.frame(names(a), round(abs(rnorm(1) * 10^5))), "temp.txt", append = TRUE, col.names = FALSE, row.names = FALSE)
			}
			if (maxSubohB > maxsnpnooh && length(b) > 2)
			{
				rhsr_rc(oh[b, b], maxsnpnooh)
			} 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)
		}
	}
	result <- rhsr_rc(oh, maxsnpnooh)
	result <- read.table("temp.txt", header = TRUE)
	file.remove("temp.txt")
	print(maxsnpnooh)
	
	result
} 

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hsphase documentation built on May 2, 2019, 3:44 p.m.