Simulated data for a 4-way cross
Simulated data for a phase-known 4-way cross, obtained using
sim.cross.
data(fake.4way)
An object of class cross. See read.cross
for 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.
Karl W Broman, broman@wisc.edu
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))
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