badorder {qtl} | R Documentation |
Simulated data for an intercross with some markers out of order.
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) plot.rf(badorder) # re-estimate map newmap <- est.map(badorder) plot.map(badorder, newmap) # assess marker order on chr 1 rip3 <- ripple(badorder, chr=1, window=3) summary(rip3)