recrate2scanone | R Documentation |
Convert the result of est.recrate()
to the format
output by R/qtl's qtl::scanone()
function.
recrate2scanone(recrate, phymap = NULL)
recrate |
A list of results from |
phymap |
A list of vectors of Mbp positions of markers |
A data frame with class "scanone"
, in the format output by qtl::scanone()
.
Karl W Broman, broman@wisc.edu
est.recrate()
pmap <- sim.map(100, n.mar=51, anchor=TRUE, include.x=FALSE, eq.spacing=TRUE)
# simulate cross
x <- sim.cross(pmap, type="bc", n.ind=501)
# estimate map for that cross
emap <- est.map(x)
# empirical estimate of recombination rate
rr <- est.recrate(emap[[1]], pmap[[1]], window=5)
# make it a list (one component per chromosome, but here just the one chromosome)
rr <- list("1"=rr)
# convert to scanone output and plot
rr_scanone <- recrate2scanone(rr)
plot(rr_scanone)
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