qtl (version 0.85-4)

read.cross.karl: Read data for a QTL experiment in Karl Broman's format

Description

Data for a QTL experiment is read from a set of files and converted into an object of class cross.

Usage

read.cross.karl(dir,genfile,mapfile,phefile)

Arguments

dir

Character string specifying the directory containing the input files.

genfile

File containing a (n.ind x n.mar) matrix of genotypes, coded 1/2/3/4/5/0 for AA/AB/BB/not BB/not AA/missing, one individual per line.

phefile

File containing a (n.ind x n.phe) matrix of phenotypes (one individual per line) with "-" denoting missing. The first line in the file should give the phenotype names.

mapfile

File containing the map information, in the following format n.chr n.mar(1) rf(1,1) rf(1,2) ...rf(1,n.mar(1)-1) mar.name(1,1) mar.name(1,2) ... mar.name(1,n.mar(1))

Value

• An object of class cross. See read.cross for details.

Details

We use the marker names to infer the chromosome names (assuming that most marker names are like D1M120 or D19M99); if the markers look like DXM*, we assume it is the X chromosome. If all genotypes are

See Also

read.cross, read.cross.mm, read.cross.gary, read.cross.csv

Examples

cross2 <- read.cross("karl",dir="Data", genfile="gen.txt",
		     phefile="phe.txt", mapfile="map.txt")