makeqtl {qtl}R Documentation

Make a qtl object

Description

This function takes a cross object and specified chromosome numbers and positions and pulls out the genotype probabilities and/or imputed genotypes at the nearest pseudomarkers, for later use by the function fitqtl.

Usage

makeqtl(cross, chr, pos, qtl.name)

Arguments

cross An object of class cross. See read.cross for details.
chr Vector indicating the chromosome for each QTL.
pos Vector (of same length as chr) indicating the positions on the chromosome to be taken. If there's no marker or pseudomarker at a position, genotypes for the nearest positions are taken.
qtl.name The user-specified name for each QTL, used in the drop-one-term ANOVA table in fitqtl. If unspecified, the names will be of the form "Chr1@10" for a QTL on Chromsome 1 at 10 cM.

Details

This function will take out the genotype probabilities and imputed genotypes if they are present in the input cross object. If both fields are missing in the input object, the function will report an error. Before running this function, the user must have first run either calc.geno or sim.geno.

Value

An object of class qtl with the following elements:

geno Imputed genotypes.
prob Genotype probabilities.
chr Input vector of chromosome numbers.
pos Input vector of chromosome positions.
n.qtl Number of QTLs.
n.ind Number of individuals.
n.gen A vector indicating the number of genotypes for each QTL.

Author(s)

Hao Wu, hao@jax.org

References

Sen, S. and Churchill, G. A. (2001) A statistical framework for quantitative trait mapping. Genetics 159, 371–387.

See Also

fitqtl, calc.genoprob, sim.geno

Examples

data(fake.f2)

# take out several QTLs and make QTL object
qc <- c(1, 6, 13)
qp <- c(25.8, 33.6, 18.63)
fake.f2 <- subset(fake.f2, chr=qc)

fake.f2 <- sim.geno(fake.f2, n.draws=8, step=2, err=0.001)
qtl <- makeqtl(fake.f2, qc, qp)

[Package qtl version 0.98-57 Index]