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######################################################################
#
# read.cross.gary.R
#
# copyright (c) 2000-2019, Karl W Broman
# last modified Dec, 2019
# first written Aug, 2000
#
# This program is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public License,
# version 3, as published by the Free Software Foundation.
#
# This 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, version 3, for more details.
#
# A copy of the GNU General Public License, version 3, is available
# at http://www.r-project.org/Licenses/GPL-3
#
# Part of the R/qtl package
# Contains: read.cross.gary
# [See read.cross.R for the main read.cross function.]
#
######################################################################
######################################################################
#
# read.cross.gary
#
# read data in Gary's format
#
######################################################################
read.cross.gary <-
function(dir,genfile,mnamesfile,chridfile,phefile,pnamesfile,mapfile,
estimate.map,na.strings)
{
# create file names
if(missing(genfile)) genfile <- "geno.dat"
if(missing(mnamesfile)) mnamesfile <- "mnames.txt"
if(missing(chridfile)) chridfile <- "chrid.dat"
if(missing(phefile)) phefile <- "pheno.dat"
if(missing(pnamesfile)) pnamesfile <- "pnames.txt"
if(missing(mapfile)) mapfile <- "markerpos.txt"
if(!missing(dir) && dir != "") {
genfile <- file.path(dir, genfile)
mnamesfile <- file.path(dir, mnamesfile)
chridfile <- file.path(dir, chridfile)
phefile <- file.path(dir, phefile)
if(!is.null(pnamesfile)) pnamesfile <- file.path(dir, pnamesfile)
if(!is.null(mapfile)) mapfile <- file.path(dir, mapfile)
}
# read data
allgeno <- as.matrix(read.table(genfile,na.strings="9"))+1
pheno <- as.matrix(read.table(phefile,na.strings=na.strings,header=FALSE))
chr <- scan(chridfile,what=character(),quiet=TRUE)
mnames <- scan(mnamesfile,what=character(),quiet=TRUE)
if(!is.null(mapfile)) {
map <- read.table(mapfile,row.names=1)
map <- map[mnames,1]
map.included <- TRUE
}
else {
map <- seq(0,by=5,len=length(mnames))
map.included <- FALSE
}
if(!is.null(pnamesfile)) pnames <- scan(pnamesfile,what=character(),quiet=TRUE)
else pnames <- paste("pheno",1:ncol(pheno),sep="")
# fix up map information
# number of chromosomes
uchr <- unique(chr)
n.chr <- length(uchr)
geno <- vector("list",n.chr)
names(geno) <- uchr
min.mar <- 1
for(i in 1:n.chr) { # loop over chromosomes
# create map
temp.map <- map[chr==uchr[i]]
# deal with any markers that didn't appear in the marker pos file
if(any(is.na(temp.map))) {
o <- (seq(along=temp.map))[is.na(temp.map)]
for(j in o) {
if(j==1 || all(is.na(temp.map[1:(j-1)]))) {
z <- min((seq(along=temp.map))[-o])
temp.map[j] <- min(temp.map,na.rm=TRUE)-(z-j+1)
}
else if(j==length(temp.map) || all(is.na(temp.map[-(1:j)]))) {
z <- max((seq(along=temp.map))[-o])
temp.map[j] <- max(temp.map,na.rm=TRUE)+(j-z+1)
}
else {
temp.map[j] <- (min(temp.map[-(1:j)],na.rm=TRUE)+
max(temp.map[1:(j-1)],na.rm=TRUE))/2
}
}
}
names(temp.map) <- mnames[chr==uchr[i]]
# pull out appropriate portion of genotype data
data <- allgeno[,min.mar:(length(temp.map)+min.mar-1),drop=FALSE]
min.mar <- min.mar + length(temp.map)
colnames(data) <- names(temp.map)
geno[[i]] <- list(data=data,map=temp.map)
if(uchr[i] == "X" || uchr[i] == "x")
class(geno[[i]]) <- "X"
else class(geno[[i]]) <- "A"
}
colnames(pheno) <- pnames
# fix up phenotype data: make things numeric that look numeric
sw2numeric_gary <-
function(x) {
pattern <- "^[ \t]*-*[0-9]*[.]*[0-9]*[ \t]*$"
n <- sum(!is.na(x))
if(length(grep(pattern,as.character(x[!is.na(x)])))==n)
return(as.numeric(as.character(x)))
else return(x)
}
pheno <- data.frame(lapply(as.data.frame(pheno), sw2numeric_gary), stringsAsFactors=TRUE)
# check that data dimensions match
n.mar1 <- sapply(geno,function(a) ncol(a$data))
n.mar2 <- sapply(geno,function(a) length(a$map))
n.phe <- ncol(pheno)
n.ind1 <- nrow(pheno)
n.ind2 <- sapply(geno,function(a) nrow(a$data))
if(any(n.ind1 != n.ind2)) {
cat(n.ind1,n.ind2,"\n")
stop("Number of individuals in genotypes and phenotypes do not match.");
}
if(any(n.mar1 != n.mar2)) {
cat(n.mar1,n.mar2,"\n")
stop("Numbers of markers in genotypes and marker names files do not match.");
}
# print some information about the amount of data read
cat(" --Read the following data:\n");
cat("\t", n.ind1, " individuals\n");
cat("\t", sum(n.mar1), " markers\n");
cat("\t", n.phe, " phenotypes\n");
# determine map type: f2 or bc or 4way?
if(max(allgeno[!is.na(allgeno)])<=2) type <- "bc"
else type <- "f2"
cross <- list(geno=geno,pheno=pheno)
class(cross) <- c(type,"cross")
# check that nothing is strange in the genotype data
if(type=="f2") max.gen <- 5
else max.gen <- 2
u <- unique(allgeno)
if(any(!is.na(u) & (u > max.gen | u < 1)))
stop("There are stange values in the genotype data : ",
paste(sort(u),collapse=":"), ".")
cross$pheno <- as.data.frame(cross$pheno, stringsAsFactors=TRUE)
# if map wasn't included, go through each chromosome and
# make first marker at 0 cM.
if(!map.included) {
for(i in 1:nchr(cross))
cross$geno[[i]]$map <- cross$geno[[i]]$map - min(cross$geno[[i]]$map)
}
# return cross + indicator of whether to run est.map
# [run est.map if map not included and estimate.map == TRUE]
list(cross, (!map.included && estimate.map) )
}
# end of read.cross.gary.R
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