######################################################################
#
# read.cross.csvs.R
#
# copyright (c) 2005-2020, Karl W Broman
# last modified Feb, 2020
# first written Oct, 2005
#
# 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.csvs
# [See read.cross.R for the main read.cross function.]
#
######################################################################
######################################################################
#
# read.cross.csvs
#
# read data in comma-delimited format, with separate files for phenotype
# and genotype data
#
######################################################################
read.cross.csvs <-
function(dir, genfile, phefile, na.strings=c("-","NA"),
genotypes=c("A","H","B","D","C"),
estimate.map=TRUE, rotate=FALSE, ...)
{
# create file names
if(missing(genfile)) genfile <- "gen.csv"
if(missing(phefile)) phefile <- "phe.csv"
if(!missing(dir) && dir != "") {
genfile <- file.path(dir, genfile)
phefile <- file.path(dir, phefile)
}
args <- list(...)
if("" %in% na.strings) {
na.strings <- na.strings[na.strings != ""]
warning("Including \"\" in na.strings will cause problems; omitted.")
}
# if user wants to use comma for decimal point, we need
if(length(args) > 0 && "dec" %in% names(args)) {
dec <- args[["dec"]]
}
else dec <- "."
# read the data file
if(length(args) < 1 || !("sep" %in% names(args))) {
# "sep" not in the "..." argument and so take sep=","
if(length(args) < 1 || !("comment.char" %in% names(args))) {
gen <- read.table(genfile, sep=",", na.strings=na.strings,
colClasses="character", fill=TRUE,
stringsAsFactors=TRUE,
blank.lines.skip=TRUE, comment.char="", ...)
pheno <- read.table(phefile, sep=",", na.strings=na.strings,
colClasses="character", fill=TRUE,
stringsAsFactors=TRUE,
blank.lines.skip=TRUE, comment.char="", ...)
}
else {
gen <- read.table(genfile, sep=",", na.strings=na.strings,
colClasses="character", fill=TRUE,
stringsAsFactors=TRUE,
blank.lines.skip=TRUE, ...)
pheno <- read.table(phefile, sep=",", na.strings=na.strings,
colClasses="character", fill=TRUE,
stringsAsFactors=TRUE,
blank.lines.skip=TRUE, ...)
}
}
else {
if(length(args) < 1 || !("comment.char" %in% names(args))) {
gen <- read.table(genfile, na.strings=na.strings,
colClasses="character", fill=TRUE,
stringsAsFactors=TRUE,
blank.lines.skip=TRUE, comment.char="", ...)
pheno <- read.table(phefile, na.strings=na.strings,
colClasses="character", fill=TRUE,
stringsAsFactors=TRUE,
blank.lines.skip=TRUE, comment.char="", ...)
}
else {
gen <- read.table(genfile, na.strings=na.strings,
colClasses="character", fill=TRUE,
stringsAsFactors=TRUE,
blank.lines.skip=TRUE, ...)
pheno <- read.table(phefile, na.strings=na.strings,
colClasses="character", fill=TRUE,
stringsAsFactors=TRUE,
blank.lines.skip=TRUE, ...)
}
}
if(rotate) {
gen <- as.data.frame(t(gen), stringsAsFactors=FALSE)
pheno <- as.data.frame(t(pheno), stringsAsFactors=FALSE)
}
# We must make the first column have the individual IDs
indname <- gen[1,1]
if(gen[3,1] == "") {
genind <- gen[-(1:3),1]
map.included <- TRUE
nondatrow <- 3 # last non-data row
}
else {
genind <- gen[-(1:2),1]
map.included <- FALSE
nondatrow <- 2 # last non-data row
}
gen <- gen[,-1,drop=FALSE]
wh <- which(pheno[1,] == indname)
if(length(wh) < 1)
stop("Can't find the individual ID column (expected '", indname,
"') in the phenotype file.")
pheind <- pheno[-1,wh[1]]
if(length(genind) == length(pheind) && all(genind == pheind)) {
if(length(genind) != length(unique(genind)))
warning("Duplicate individual IDs")
}
else {
if(any(is.na(genind)) && any(is.na(pheind)))
stop("There are missing genotype and phenotype IDs")
else if(any(is.na(genind)))
stop("There are missing genotype IDs")
else if(any(is.na(pheind)))
stop("There are missing phenotype IDs")
if(length(genind) != length(unique(genind)) && length(pheind) != length(unique(pheind)))
stop("There are duplicate genotype and phenotype IDs, and they don't all line up.")
else if(length(genind) != length(unique(genind)))
stop("There are duplicate genotype IDs, and the genotype and phenotype IDs don't all line up.")
else if(length(pheind) != length(unique(pheind)))
stop("There are duplicate phenotype IDs, and the genotype and phenotype IDs don't all line up.")
mgp <- match(genind, pheind)
if(any(is.na(mgp))) { # individuals with genotypes but no phenotypes
n.add <- sum(is.na(mgp))
pheind <- c(pheind, genind[is.na(mgp)])
pheno <- rbind(pheno, matrix(rep(NA, n.add*ncol(pheno)), ncol=ncol(pheno)))
pheno[-1, wh[1]] <- pheind
warning(n.add, " individuals with genotypes but no phenotypes\n ", paste(genind[is.na(mgp)], collapse="|"), "\n")
}
mpg <- match(pheind, genind)
if(any(is.na(mpg))) {
n.add <- sum(is.na(mpg))
genind <- c(genind, pheind[is.na(mpg)])
genadd <- matrix(rep(NA, n.add*ncol(gen)), ncol=ncol(gen))
colnames(genadd) <- colnames(gen)
gen <- rbind(gen, genadd)
warning(n.add, " individuals with phenotypes but no genotypes\n ", paste(pheind[is.na(mpg)], collapse="|"), "\n")
}
mgp <- match(genind, pheind)
pheind <- pheind[mgp]
pheno <- pheno[1+c(0,mgp),,drop=FALSE]
}
n.phe <- ncol(pheno)
if(map.included) {
map <- asnumericwithdec(unlist(gen[3,]), dec=dec)
if(any(is.na(map))) {
temp <- unique(unlist(gen[3,])[is.na(map)])
stop("There are missing marker positions.\n",
" In particular, we see these value(s): ",
paste("\"",paste(temp,collapse="\",\"",sep=""),"\"",collapse=" ",sep=""),
" at position(s): ",
paste(which(is.na(map)),colapse=",",sep=""),sep="")
}
}
else
map <- rep(0,ncol(gen))
colnames_pheno <- unlist(pheno[1,])
pheno <- apply(pheno, 2, function(a) { a[!is.na(a) & a==""] <- NA; a })
pheno <- as.data.frame(pheno[-1,], stringsAsFactors=TRUE)
colnames(pheno) <- colnames_pheno
# replace empty cells with NA
gen <- sapply(gen,function(a) { a[!is.na(a) & a==""] <- NA; a })
# pull apart phenotypes, genotypes and map
mnames <- unlist(gen[1,])
if(any(is.na(mnames)))
stop("There are missing marker names. Check column(s) ",paste(which(is.na(mnames))+1+n.phe,collapse=","),sep="")
chr <- unlist(gen[2,])
if(any(is.na(chr)))
stop("There are missing chromosome IDs. Check column(s) ",paste(which(is.na(chr))+1+n.phe,collapse=","),sep="")
if(any(is.na(chr))) {
na.positions <- which(is.na(chr))
na.positions.str <- ""
if (length(na.positions)<10) {
na.positions.str <- paste(" at position(s) ",
paste(na.positions,collapse=",",sep=""),sep="")
}
stop("There are ", length(na.positions), " missing chromosome IDs",
na.positions.str, ".")
}
# look for strange entries in the genotype data
if(length(genotypes) > 0) {
temp <- unique(as.character(gen[-(1:nondatrow),,drop=FALSE]))
temp <- temp[!is.na(temp)]
wh <- !(temp %in% genotypes)
if(any(wh)) {
warn <- "The following unexpected genotype codes were treated as missing.\n "
ge <- paste("|", paste(temp[wh],collapse="|"),"|",sep="")
warn <- paste(warn,ge,"\n",sep="")
warning(warn)
}
# convert genotype data
allgeno <- matrix(match(gen[-(1:nondatrow),,drop=FALSE],genotypes),
ncol=ncol(gen))
}
else
allgeno <- matrix(as.numeric(gen[-(1:nondatrow),,drop=FALSE]),
ncol=ncol(gen))
pheno <- data.frame(lapply(pheno, sw2numeric, dec=dec), stringsAsFactors=TRUE)
# re-order the markers by chr and position
# try to figure out the chr labels
if(all(chr %in% c(1:999,"X","x"))) { # 1...19 + X
tempchr <- chr
tempchr[chr=="X" | chr=="x"] <- 1000
tempchr <- as.numeric(tempchr)
if(map.included) neworder <- order(tempchr, map)
else neworder <- order(tempchr)
}
else {
# don't let it reorder the chromosomes
tempchr <- factor(chr, levels=unique(chr))
if(map.included) neworder <- order(tempchr, map)
else neworder <- order(tempchr)
}
chr <- chr[neworder]
map <- map[neworder]
allgeno <- allgeno[,neworder,drop=FALSE]
mnames <- mnames[neworder]
# fix up dummy map
if(!map.included) {
map <- split(rep(0,length(chr)),chr)[unique(chr)]
map <- unlist(lapply(map,function(a) seq(0,length=length(a),by=5)))
names(map) <- NULL
}
# 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
allautogeno <- NULL
for(i in 1:n.chr) { # loop over chromosomes
# create map
temp.map <- map[chr==uchr[i]]
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"
if(is.null(allautogeno)) allautogeno <- data
else allautogeno <- cbind(allautogeno,data)
}
}
if(is.null(allautogeno)) allautogeno <- allgeno
# 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$data))
if(any(n.ind1 != n.ind2)) {
cat(n.ind1,n.ind2,"\n")
stop("Number of individuals in genotypes and phenotypes do not match.");
}
if(any(n.mar1 != n.mar2)) {
cat(n.mar1,n.mar2,"\n")
stop("Numbers of markers in genotypes and marker names files do not match.");
}
# print some information about the amount of data read
cat(" --Read the following data:\n");
cat("\t", n.ind1, " individuals\n");
cat("\t", sum(n.mar1), " markers\n");
cat("\t", n.phe, " phenotypes\n");
if(all(is.na(allgeno)))
warning("There is no genotype data!\n")
# determine map type: f2 or bc or 4way?
if(all(is.na(allgeno))) warning("There is no genotype data!\n")
if(all(is.na(allautogeno)) || max(allautogeno,na.rm=TRUE)<=2) type <- "bc"
else if(max(allautogeno,na.rm=TRUE)<=5) type <- "f2"
else type <- "4way"
cross <- list(geno=geno,pheno=pheno)
class(cross) <- c(type,"cross")
# check that nothing is strange in the genotype data
if(type=="f2") max.gen <- 5
else if(type=="bc") max.gen <- 2
else max.gen <- 14
# check that markers are in proper order
# if not, fix up the order
for(i in 1:n.chr) {
if(any(diff(cross$geno[[i]]$map)<0)) {
o <- order(cross$geno[[i]]$map)
cross$geno[[i]]$map <- cross$geno[[i]]$map[o]
cross$geno[[i]]$data <- cross$geno[[i]]$data[,o,drop=FALSE]
}
}
# estimate genetic map
if(estimate.map && !map.included) estmap <- TRUE
else estmap <- FALSE
# return cross + indicator of whether to run est.map
list(cross,estmap)
}
# end of read.cross.csvs.R
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