qtl (version 1.66)

badorder: An intercross with misplaced markers

Description

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

Usage

data(badorder)

Format

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

Author

Karl W Broman,

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.

See Also

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

Examples

data(badorder)
badorder <- subset(badorder,chr=1)

# 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)