######################################################################
#
# readMWril.R
#
# copyright (c) 2009-2020, Karl W Broman
# last modified Feb, 2020
# first written Apr, 2009
#
# 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: readMWril
#
######################################################################
######################################################################
#
# readMWril
#
# read multi-way RIL data in comma-delimited format,
# with a separate file for the founder genotypes, and possible a
# separate file for the phenotype data.
#
######################################################################
readMWril <-
function(dir, rilfile, founderfile,
type=c("ri4self", "ri4sib", "ri8self", "ri8selfIRIP1", "ri8sib", "bgmagic16"),
na.strings=c("-","NA"), rotate=FALSE,
...)
{
# create file names
if(missing(rilfile) || missing(founderfile))
stop("Need to specify rilfile and founderfile.")
if(!missing(dir) && dir != "") {
rilfile <- file.path(dir, rilfile)
founderfile <- file.path(dir, founderfile)
}
type <- match.arg(type)
args <- list(...)
# 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(rilfile, sep=",", na.strings=na.strings,
colClasses="character", fill=TRUE,
stringsAsFactors=TRUE,
blank.lines.skip=TRUE, comment.char="", ...)
founder <- read.table(founderfile, sep=",", na.strings=na.strings,
colClasses="character", fill=TRUE,
stringsAsFactors=TRUE,
blank.lines.skip=TRUE, comment.char="", ...)
}
else {
gen <- read.table(rilfile, sep=",", na.strings=na.strings,
colClasses="character", fill=TRUE,
stringsAsFactors=TRUE,
blank.lines.skip=TRUE, ...)
founder <- read.table(founderfile, 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(rilfile, na.strings=na.strings,
colClasses="character", fill=TRUE,
stringsAsFactors=TRUE,
blank.lines.skip=TRUE, comment.char="", ...)
founder <- read.table(founderfile, na.strings=na.strings,
colClasses="character", fill=TRUE,
stringsAsFactors=TRUE,
blank.lines.skip=TRUE, comment.char="", ...)
}
else {
gen <- read.table(rilfile, na.strings=na.strings,
colClasses="character", fill=TRUE,
stringsAsFactors=TRUE,
blank.lines.skip=TRUE, ...)
founder <- read.table(founderfile, na.strings=na.strings,
colClasses="character", fill=TRUE,
stringsAsFactors=TRUE,
blank.lines.skip=TRUE, ...)
}
}
if(rotate) {
gen <- as.data.frame(t(gen), stringsAsFactors=FALSE)
founder <- as.data.frame(t(founder), stringsAsFactors=FALSE)
}
rn <- founder[-1,1]
cn <- founder[1,-1]
founder <- founder[-1,-1, drop=FALSE]
founder <- matrix(as.numeric(unlist(founder)), ncol=length(cn))
dimnames(founder) <- list(rn, cn)
# determine number of phenotypes based on initial blanks in row 2
n <- ncol(gen)
temp <- rep(FALSE,n)
for(i in 1:n) {
temp[i] <- all(gen[2,1:i]=="")
if(!temp[i]) break
}
if(!any(temp)) # no phenotypes!
stop("You must include at least one phenotype (e.g., an index).")
n.phe <- max((1:n)[temp])
# Is map included? yes if first n.phe columns in row 3 are all blank
if(all(!is.na(gen[3,1:n.phe]) & gen[3,1:n.phe]=="")) {
map.included <- TRUE
map <- asnumericwithdec(unlist(gen[3,-(1:n.phe)]), dec=dec)
if(any(is.na(map)))
stop("There are missing marker positions.")
nondatrow <- 3
}
else {
map.included <- FALSE
map <- rep(0,ncol(gen)-n.phe)
nondatrow <- 2 # last non-data row
}
pheno <- as.data.frame(gen[-(1:nondatrow),1:n.phe,drop=FALSE], stringsAsFactors=FALSE)
colnames(pheno) <- as.character(gen[1,1:n.phe])
# replace empty cells with NA
gen <- sapply(gen,function(a) { a[!is.na(a) & a==""] <- NA; a })
# pull apart phenotypes, genotypes and map
mnames <- gen[1,-(1:n.phe)]
if(any(is.na(mnames))) stop("There are missing marker names.")
chr <- gen[2,-(1:n.phe)]
if(any(is.na(chr))) stop("There are missing chromosome IDs.")
gen <- matrix(as.numeric(gen[-(1:nondatrow),-(1:n.phe)]),
ncol=ncol(gen)-n.phe)
pheno <- data.frame(lapply(pheno, sw2numeric, dec=dec), stringsAsFactors=TRUE)
n.str <- nrow(founder)
if(type == "ri8selfIRIP1"){
}
else if(!("cross" %in% names(pheno))) {
warning("Need a phenotype named \"cross\"; assuming all come from the cross ",
paste(LETTERS[1:n.str], collapse="x"))
crosses <- matrix(1:n.str, ncol=n.str, nrow=nrow(gen), byrow=TRUE)
}
else {
pheno$cross <- as.character(pheno$cross)
if(any(nchar(pheno$cross) != n.str))
stop("Mismatches in length of \"cross\" phenotype.")
thecross <- matrix(unlist(strsplit(pheno$cross, "")), byrow=TRUE, ncol=n.str)
crosses <- matrix(NA, ncol=n.str, nrow=nrow(gen))
for(i in 1:nrow(thecross))
crosses[i,] <- match(thecross[i,], LETTERS[1:n.str])
if(any(is.na(crosses)))
stop("Problems in the \"cross \" phenotype.")
}
# check founder data matches in dimension
if(ncol(founder) != ncol(gen))
stop("Different numbers of markers in RIL and founder files.")
if(any(colnames(founder) != mnames)) {
cnf <- colnames(founder)
if(any(is.na(match(cnf, mnames))) || any(is.na(match(mnames, cnf))))
stop("Mismatch in markers in RIL and founder files.")
founder <- founder[,match(mnames, cnf),drop=FALSE]
}
wh <- which(is.na(gen))
missingval <- min(as.numeric(c(gen, founder)), na.rm=TRUE)-1
gen[wh] <- missingval
founder[is.na(founder)] <- missingval
d <- dim(gen)
if(type == "ri8selfIRIP1")
{
gen <-
.C("R_reviseMWrilNoCross",
as.integer(d[1]),
as.integer(d[2]),
as.integer(n.str),
as.integer(founder),
gen=as.integer(gen),
as.integer(missingval),
PACKAGE="qtl")$gen
}
else
{
gen <-
.C("R_reviseMWril",
as.integer(d[1]),
as.integer(d[2]),
as.integer(n.str),
as.integer(founder),
gen=as.integer(gen),
as.integer(crosses),
as.integer(missingval),
PACKAGE="qtl")$gen
}
gen[wh] <- NA
gen <- matrix(gen, nrow=d[1])
gen[gen==0 | gen==(2^n.str-1)] <- NA
# 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)
chr <- chr[neworder]
map <- map[neworder]
gen <- gen[,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
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 <- gen[,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"
}
cross <- list(geno=geno,pheno=pheno)
# 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$data))
if(any(n.ind1 != n.ind2)) {
cat(n.ind1,n.ind2,"\n")
stop("Number of individuals in genotypes and phenotypes do not match.");
}
if(any(n.mar1 != n.mar2)) {
cat(n.mar1,n.mar2,"\n")
stop("Numbers of markers in genotypes and marker names files do not match.");
}
# print some information about the amount of data read
cat(" --Read the following data:\n");
cat("\t", n.ind1, " individuals\n");
cat("\t", sum(n.mar1), " markers\n");
cat("\t", n.phe, " phenotypes\n");
if(all(is.na(gen)))
warning("There is no genotype data!\n")
if(type != "ri8selfIRIP1")
{
cross$cross <- crosses
}
# save founder genotypes in data
founder[founder==missingval] <- NA
ua <- apply(founder, 2, function(a) unique(a[!is.na(a)]))
nua <- sapply(ua, length)
if(all(nua <= 2)) { # re-code as 0/1
for(i in 1:ncol(founder)) {
if(nua[i]==1)
founder[!is.na(founder[,i]),i] <- 0
else if(nua[i]==2) {
founder[!is.na(founder[,i]) & founder[,i]==ua[[i]][1],i] <- 0
founder[!is.na(founder[,i]) & founder[,i]==ua[[i]][2],i] <- 1
}
}
}
cross$founderGeno <- founder
class(cross) <- c(type, "cross")
# check data
summary(cross)
cross
}
# end of readMWril.R
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