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######################################################################
#
# write.cross.R
#
# copyright (c) 2001-7, Karl W Broman and Hao Wu
# last modified Sep, 2007
# first written Feb, 2001
# Licensed under the GNU General Public License version 2 (June, 1991)
#
# Part of the R/qtl package
# Contains: write.cross, write.cross.mm, write.cross.csv,
# write.cross.gary, fixX4write
# [See qtlcart_io.R for write.cross.qtlcart]
#
######################################################################
######################################################################
#
# write.cross: Wrapper for the other write.cross functions
#
######################################################################
write.cross <-
function(cross, format=c("csv", "csvr", "csvs", "csvsr", "mm", "qtlcart", "gary"),
filestem="data", chr, digits=5)
{
if(!any(class(cross) == "cross"))
stop("Input should have class \"cross\".")
format <- match.arg(format)
if(!missing(chr)) cross <- subset(cross,chr=chr)
# revise X data
chrtype <- sapply(cross$geno,class)
crosstype <- class(cross)[1]
if((crosstype=="bc" || crosstype=="f2") &&
any(chrtype=="X")) {
sexpgm <- getsex(cross)
sex <- sexpgm$sex
pgm <- sexpgm$pgm
for(i in which(chrtype=="X"))
cross$geno[[i]]$data <- fixX4write(cross$geno[[i]]$data,sex,pgm,crosstype)
}
if(format=="csv") write.cross.csv(cross,filestem,digits,FALSE,FALSE)
else if(format=="csvr") write.cross.csv(cross,filestem,digits,TRUE,FALSE)
else if(format=="csvs") write.cross.csv(cross,filestem,digits,FALSE,TRUE)
else if(format=="csvsr") write.cross.csv(cross,filestem,digits,TRUE,TRUE)
else if(format=="mm") write.cross.mm(cross,filestem,digits)
else if(format=="qtlcart") write.cross.qtlcart(cross, filestem)
else write.cross.gary(cross, digits)
}
######################################################################
#
# write.cross.mm: Write data for an experimental cross in Mapmaker
# format
#
# creates two files: "raw" file with geno & pheno data
# "prep" file with map information
#
######################################################################
write.cross.mm <-
function(cross, filestem="data", digits=5)
{
n.ind <- nind(cross)
tot.mar <- totmar(cross)
n.phe <- nphe(cross)
n.chr <- nchr(cross)
n.mar <- nmar(cross)
type <- class(cross)[1]
if(type=="riself" || type=="risib") type <- "bc"
if(type != "f2" && type != "bc")
stop("write.cross.mm only works for intercross, backcross and RI data.")
# write genotype and phenotype data
file <- paste(filestem, ".raw", sep="")
# write experiment type
if(type == "f2")
write("data type f2 intercross", file, append=FALSE)
else
write("data type f2 backcross", file, append=FALSE)
# write numbers of progeny, markers and phenotypes
write(paste(n.ind, tot.mar, n.phe), file, append=TRUE)
# max length of marker name
mlmn <- max(nchar(unlist(lapply(cross$geno,function(a) colnames(a$data)))))+1
# write marker data
for(i in 1:n.chr) {
for(j in 1:n.mar[i]) {
mn <- paste("*", colnames(cross$geno[[i]]$data)[j], sep="")
if(nchar(mn) < mlmn)
mn <- paste(mn,paste(rep(" ", mlmn-nchar(mn)),collapse=""),sep="")
g <- cross$geno[[i]]$data[,j]
x <- rep("", n.ind)
x[is.na(g)] <- "-"
x[!is.na(g) & g==1] <- "A"
x[!is.na(g) & g==2] <- "H"
if(type == "f2") {
x[!is.na(g) & g==3] <- "B"
x[!is.na(g) & g==4] <- "D"
x[!is.na(g) & g==5] <- "C"
}
if(n.ind < 60)
write(paste(mn, paste(x,collapse="")), file, append=TRUE)
else {
lo <- seq(1,n.ind-1,by=60)
hi <- c(lo[-1]-1,n.ind)
for(k in seq(along=lo)) {
if(k==1) write(paste(mn,paste(x[lo[k]:hi[k]],collapse="")),file,append=TRUE)
else write(paste(paste(rep(" ", mlmn),collapse=""),
paste(x[lo[k]:hi[k]],collapse="")),file,append=TRUE)
}
}
}
} # end writing marker data
# max length of phenotype name
mlpn <- max(nchar(colnames(cross$pheno)))+1
# write phenotypes
for(i in 1:n.phe) {
pn <- paste("*",colnames(cross$pheno)[i],sep="")
if(nchar(pn) < mlpn)
pn <- paste(pn, paste(rep(" ", mlpn-nchar(pn)),collapse=""),sep="")
if(!is.factor(cross$pheno[,i]))
x <- as.character(round(cross$pheno[,i],digits))
else
x <- as.character(cross$pheno[,i])
x[is.na(x)] <- "-"
if(n.ind < 10)
write(paste(pn, paste(x,collapse="")), file, append=TRUE)
else {
lo <- seq(1,n.ind-1,by=10)
hi <- c(lo[-1]-1,n.ind)
for(k in seq(along=lo)) {
if(k==1) write(paste(pn,paste(x[lo[k]:hi[k]],collapse=" ")),file,append=TRUE)
else write(paste(paste(rep(" ", mlpn),collapse=""),
paste(x[lo[k]:hi[k]],collapse=" ")),file,append=TRUE)
}
}
}
# make "prep" file with map information
file <- paste(filestem, ".prep", sep="")
for(i in 1:n.chr) {
cname <- paste("chr", names(cross$geno)[i], sep="")
line <- paste("make chromosome", cname)
if(i==1) write(line, file, append=FALSE)
else write(line, file, append=TRUE)
mn <- names(cross$geno[[i]]$map)
# dis <- round(diff(cross$geno[[i]]$map),2)
# dis <- paste("=", dis, sep="")
# write(paste(paste("sequence", mn[1]), paste(dis,mn[-1],collapse=" ")),
# file, append=TRUE)
write(paste(paste("sequence", mn[1]), paste(mn[-1],collapse=" ")),
file, append=TRUE)
write(paste("anchor", cname), file, append=TRUE)
write(paste("framework", cname), file, append=TRUE)
}
}
######################################################################
#
# write.cross.csv: Write data for an experimental cross in
# comma-delimited format (the same format as is read
# by read.cross.csv)
#
######################################################################
write.cross.csv <-
function(cross, filestem="data", digits=5, rotate=FALSE, split=FALSE)
{
type <- class(cross)[1]
if(type != "f2" && type != "bc" && type != "riself" && type != "risib")
stop("write.cross.csv only works for intercross, backcross and RI data.")
if(!split)
file <- paste(filestem, ".csv", sep="")
else {
genfile <- paste(filestem, "_gen.csv", sep="")
phefile <- paste(filestem, "_phe.csv", sep="")
}
if(split) { # split files; need individual IDs
id <- getid(cross)
if(is.null(id)) {
cross$pheno$id <- 1:nind(cross)
id <- getid(cross)
}
id.col <- which(colnames(cross$pheno)==attr(id,"phenam"))
}
n.ind <- nind(cross)
tot.mar <- totmar(cross)
n.phe <- nphe(cross)
n.chr <- nchr(cross)
n.mar <- nmar(cross)
geno <- matrix(ncol=tot.mar,nrow=n.ind)
# allele codes to use
if("alleles" %in% names(attributes(cross))) {
alle <- attr(cross, "alleles")
alleles <- c(paste(alle[1],alle[1],sep=""),
paste(alle[1],alle[2],sep=""),
paste(alle[2],alle[2],sep=""),
paste("not ", alle[2],alle[2],sep=""),
paste("not ", alle[1],alle[1],sep=""))
}
else alleles <- c("A","H","B","D","C")
firstmar <- 1
for(i in 1:n.chr) {
# replace allele numbers with
geno[,firstmar:(firstmar+n.mar[i]-1)] <-
alleles[match(cross$geno[[i]]$data,1:5)]
firstmar <- firstmar + n.mar[i]
}
if(any(is.na(geno))) geno[is.na(geno)] <- "-"
pheno <- matrix(as.character(round(unlist(cross$pheno),digits)),nrow=n.ind)
# factors: should be character by the levels rather than something like "1", "2", etc.
for(i in 1:nphe(cross))
if(is.factor(cross$pheno[,i])) pheno[,i] <- as.character(cross$pheno[,i])
if(any(is.na(pheno))) pheno[is.na(pheno)] <- "-"
thedata <- cbind(pheno,geno)
colnames(thedata) <- c(colnames(cross$pheno),
unlist(lapply(cross$geno, function(a) colnames(a$data))))
chr <- rep(names(cross$geno),n.mar)
pos <- unlist(lapply(cross$geno,function(a) a$map))
chr <- c(rep("",n.phe),chr)
pos <- c(rep("",n.phe),as.character(round(pos,digits)))
# put it all together
thenames <- colnames(thedata)
thedata <- matrix(as.character(thedata), ncol=ncol(thedata))
thedata <- rbind(thenames, chr, pos, thedata)
if(!split) {
if(!rotate)
write.table(thedata, file, quote=FALSE, sep=",",
row.names=FALSE, col.names=FALSE)
else
write.table(t(thedata), file, quote=FALSE, sep=",",
row.names=FALSE, col.names=FALSE)
}
else { # split files: one for phenotypes and one for genotypes
n.phe <- nphe(cross)
phe <- thedata[-(2:3),1:n.phe]
gen <- cbind(thedata[,id.col], thedata[,-(1:n.phe)])
if(!rotate) {
write.table(gen, genfile, quote=FALSE, sep=",",
row.names=FALSE, col.names=FALSE)
write.table(phe, phefile, quote=FALSE, sep=",",
row.names=FALSE, col.names=FALSE)
}
else {
write.table(t(gen), genfile, quote=FALSE, sep=",",
row.names=FALSE, col.names=FALSE)
write.table(t(phe), phefile, quote=FALSE, sep=",",
row.names=FALSE, col.names=FALSE)
}
}
}
######################################################################
#
# write.cross.gary: Write data for an experimental cross in
# Gary's format. There will be 6 output files, they are:
# chrid.dat - chromosome ids
# markerpos.txt - marker position
# mnames.txt - marker names
# geno.data - genotypes
# pheno.data - phenotypes
# pnames.txt - phenotype names
#
######################################################################
write.cross.gary <-
function(cross, digits)
{
# local variables
n.ind <- nind(cross)
tot.mar <- totmar(cross)
n.phe <- nphe(cross)
n.chr <- nchr(cross)
n.mar <- nmar(cross)
# chromosome ids
chrid <- NULL
for(i in 1:n.chr) {
# the name for this chromosome
chrname <- names(cross$geno[i])
# convert to number (why?)
# if(chrname=="X") chrname <- 20
# else chrname <- as.numeric(chrname)
chrid <- c(chrid, rep(chrname, n.mar[i]))
}
write.table(chrid, file="chrid.dat", quote=FALSE, row.names=FALSE,
col.names=FALSE)
# marker position file
markpos <- NULL
for(i in 1:n.chr)
markpos <- c(markpos, cross$geno[[i]]$map)
write.table(markpos, file="markerpos.txt", quote=FALSE, sep="\t",
row.names=TRUE, col.names=FALSE)
# marker names
mnames <- names(markpos)
write.table(mnames, file="mnames.txt", quote=FALSE, row.name=FALSE,
col.names=FALSE)
# genotype
geno <- NULL
for(i in 1:n.chr)
geno <- cbind(geno, cross$geno[[i]]$data)
# note that gary's format codes genotype from 0
# and 9 is for NA
geno <- geno - 1 # note NA will still be NA
write.table(geno, file="geno.dat", quote=FALSE, row.name=FALSE,
col.name=FALSE, sep="\t", na="9")
# phenotype
pheno <- matrix(as.character(round(unlist(cross$pheno),digits)),nrow=n.ind)
for(i in 1:nphe(cross))
if(is.factor(cross$pheno[,i])) pheno[,i] <- as.character(cross$pheno[,i])
write.table(pheno, file="pheno.dat", quote=FALSE, row.names=FALSE,
col.names=FALSE, sep="\t", na="-999")
# phenotype names
write.table(names(cross$pheno), file="pnames.txt", quote=FALSE,
row.names=FALSE, col.names=FALSE, sep="\t", na="-999")
}
######################################################################
# fixX4write
######################################################################
fixX4write <-
function(geno,sex,pgm,crosstype)
{
# males
if(!is.null(sex) & any(sex==1)) {
temp <- geno[sex==1,,drop=FALSE]
temp[temp==2] <- 3
geno[sex==1,] <- temp
}
if(crosstype == "f2") {
# females
if(!is.null(pgm)) {
if(!is.null(sex)) {
if(any(pgm==1 & sex==0)) {
temp <- geno[sex==0 & pgm==1,,drop=FALSE]
temp[temp==1] <- 3
geno[sex==0 & pgm==1,] <- temp
}
}
else { # assume all females
if(any(pgm==1)) {
temp <- geno[pgm==1,,drop=FALSE]
temp[temp==1] <- 3
geno[pgm==1,] <- temp
}
}
}
}
geno
}
# end of write.cross.R
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