read.cross {qtl}R Documentation

Read data for a QTL experiment

Description

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

Usage

read.cross(format=c("csv","mm","gary","karl"), ...)

Arguments

format Specifies the format of the data ("csv", "mm", "gary", or "karl").
... All other arguments are passed to functions specific to the data format.

Details

This function calls either read.cross.csv, read.cross.mm, read.cross.gary, or read.cross.karl, according to the specified format.

Value

An object of class cross, which is a list with two components:

geno This is a list with elements corresponding to chromosomes.

names(geno) contains the names of the chromsomes.

Each chromosome is itself a list, and is given class A or X according to whether it is autosomal or the X chromosome.

There are two components for each chromosome:
data, a matrix whose rows are individuals and whose columns are markers
map, either a vector of marker positions (in cM) or a matrix of dim (2 x n.mar) where the rows correspond to marker positions in female and male genetic distance, respectively.

The genotype data for a backcross is coded as follows: 0 = missing, 1 = AA, 2 = AB.

For an F2 intercross, the coding is 0 = missing, 1 = AA, 2 = AB, 3 = BB, 4 = not BB (ie AA or AB; D in mapmaker/qtl), 5 = not AA (ie AB or BB; C in mapmaker/qtl).

For a 4-way cross, the mother and father are assumed to have genotypes AB and CD, respectively. The genotype data for the progeny is assumed to be phase-known, with the following coding scheme: 0 = missing, 1 = AC, 2 = BC, 3 = AD, 4 = BD, 5 = A = AC or AD, 6 = B = BC or BD, 7 = C = AC or BC, 8 = D = AD or BD, 9 = AC or BD, 10 = AD or BC.
pheno Matrix of size (n.ind x n.phe) containing the phenotypes

Author(s)

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

See Also

read.cross.csv, read.cross.gary, read.cross.mm, read.cross.karl, fake.bc, fake.f2, fake.4way, listeria, hyper

Examples

cross1 <- read.cross("karl",dir="Data", genfile="gen.txt",
                     phefile="phe.txt", mapfile="map.txt")
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