read.cross.karl {qtl}R Documentation

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))
n.mar(2)
...
etc.

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 <= 2, we assume it is a backcross, otherwise it is assumed to be an intercross. We weren't thinking about 4-way crosses, and so this format doesn't work for that type of cross.

Value

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

Author(s)

Karl W Broman, kbroman@jhsph.edu
http://biosun01.biostat.jhsph.edu/~kbroman/software/qtl.html

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")
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