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qtl (version 1.70)

badorder: An intercross with misplaced markers

Description

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

Usage

data(badorder)

Arguments

Format

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

Author

Karl W Broman, broman@wisc.edu

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

Run this code
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)

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