badorder: An intercross with misplaced markers

In kbroman/qtl: Tools for Analyzing QTL Experiments

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.

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.

Author(s)

Karl W Broman, [e-mail]

See Also

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

Examples

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)

kbroman/qtl documentation built on Jan. 13, 2024, 10:14 p.m.