fake.4way: Simulated data for a 4-way cross

In qtl: Tools for Analyzing QTL Experiments

Simulated data for a 4-way cross

Description

Simulated data for a phase-known 4-way cross, obtained using sim.cross.

Usage

data(fake.4way)

Format

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

Details

There are 250 individuals typed at 157 markers, including 8 on the X chromosome.

There are two phenotypes (including sex, for which 0=female and 1=male). The quantitative phenotype is affected by three QTLs: two on chromosome 2 at positions 10 and 25 cM on the female genetic map, and one on chromosome 7 at position 40 cM on the female map.

Author(s)

Karl W Broman, [e-mail]

See Also

sim.cross, fake.bc, fake.f2, listeria, hyper, bristle3, bristleX

Examples

data(fake.4way)

plot(fake.4way)
summary(fake.4way)

# estimate recombination fractions
fake.4way <- est.rf(fake.4way)
plotRF(fake.4way)

# estimate genetic maps
ssmap <- est.map(fake.4way, verbose=TRUE)
samap <- est.map(fake.4way, sex.sp=FALSE, verbose=TRUE)
plot(ssmap, samap)

# error lod scores
fake.4way <- calc.genoprob(fake.4way, err=0.01)
fake.4way <- calc.errorlod(fake.4way, err=0.01)
top.errorlod(fake.4way, cutoff=2.5)

# genome scan
fake.4way <- calc.genoprob(fake.4way, step=2.5)
out.hk <- scanone(fake.4way, method="hk")
out.em <- scanone(fake.4way, method="em")
plot(out.em,out.hk,chr=c(2,7))

qtl documentation built on Nov. 28, 2023, 1:09 a.m.