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# Mega2: Manipulation Environment for Genetic Analysis
# Copyright (C) 1999-2013 Robert Baron, Charles P. Kollar,
# Nandita Mukhopadhyay, Lee Almasy, Mark Schroeder, William P. Mulvihill,
# Daniel E. Weeks, and University of Pittsburgh
#
# This file is part of the Mega2 program, which 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.
#
# Mega2 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, write to the Free Software
# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
#
# For further information contact:
# Daniel E. Weeks
# e-mail: weeks@pitt.edu
#
# ===========================================================================
# CREATE TWO FORMAT GENOMEGRAPHS FILES CONTAINING EITHER CHROMOSOME BASE OR MARKER ID
genomeplot <- function(gg.data)
{
# Read in genome data file
if (file.exists(gg.data) == TRUE) { dat_chr <- read.table(gg.data, header=T) } else {
warning(paste("File", gg.data, "does not", "exist!", sep=" "))
return(FALSE)
}
dat_id <- dat_chr[dat_chr[,2]!="-", ]
n <- length(dat_chr) - 3
if (n == 1) {
# Create chromosome table
w_chr <- dat_chr[!is.na(dat_chr[,4]),]
# Define the length of chromosome base table
chr <- paste("chr", w_chr[,1], sep="")
chr_tab <- data.frame(chr, w_chr[,3], w_chr[,4])
names(chr_tab) <- c("Chromosome", "Position", names(w_chr)[4])
write.table(chr_tab, file="GG.positions.all", append=F, quote=F, row.names=F, col.names=T, sep="\t")
# Create id table
w_id <- dat_id[!is.na(dat_id[,4]),]
id_tab <- data.frame(as.character(w_id[,2]), w_id[,4])
names(id_tab) <- c("Marker", names(w_id)[4])
write.table(id_tab, file="GG.markers.all", append=F, quote=F, row.names=F, col.names=T, sep="\t")
} else {
for (i in 1:n) {
# Create chromosome table
w_chr <- dat_chr[!is.na(dat_chr[,i+3]),]
if (length(w_chr[,1]) != 0) {
# Define the length of chromosome base table
chr <- paste("chr", w_chr[,1], sep="")
chr_t <- paste("GG.positions", names(w_chr)[i+3], "all", sep=".")
chr_tab <- data.frame(chr, w_chr[,3], w_chr[,i+3])
names(chr_tab) <- c("Chromosome", "Position", names(w_chr)[i+3])
write.table(chr_tab, file=chr_t, append=F, quote=F, row.names=F, col.names=T, sep="\t")
}
# Create id table
w_id <- dat_id[!is.na(dat_id[,i+3]),]
if (length(w_id[,1]) != 0) {
id_t <- paste("GG.markers", names(w_chr)[i+3], "all", sep=".")
id_tab <- data.frame(as.character(w_id[,2]), w_id[,i+3])
names(id_tab) <- c("Marker", names(w_id)[i+3])
write.table(id_tab, file=id_t, append=F, quote=F, row.names=F, col.names=T, sep="\t")
}
}
}
return(TRUE)
}
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