badorder: An intercross with misplaced markers
In byandell/qtl: Tools for analyzing QTL experiments

Description Usage Format Details Author(s) See Also Examples

Simulated data for an intercross with some markers out of order.

1	data(badorder)

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

There are 250 F2 individuals typed at a total of 36 markers on four chromosomes. The data were simulated with QTLs at the center of chromosomes 1 and 3.

The order of several markers on chromosome 1 is incorrect. Markers on chromosomes 2 and 3 are switched.

Karl W Broman, kbroman@biostat.wisc.edu

est.rf, ripple, est.map, sim.cross

data(badorder)

# estimate recombination fractions
badorder <- est.rf(badorder)
plotRF(badorder)

# re-estimate map
newmap <- est.map(badorder)
plotMap(badorder, newmap)

# assess marker order on chr 1
rip3 <- ripple(badorder, chr=1, window=3)
summary(rip3)