Usage
calc.pairprob(cross, step=0, off.end=0, error.prob=0,
map.function=c("haldane","kosambi","c-f"))
checkcovar(cross, pheno.col, addcov, intcov)
convert.cross(cross)
create.map(map, step, off.end)
discan(cross, pheno.col=1, method=c("em","mr"),
maxit=4000, tol=1e-4)
imf.cf(r)
imf.h(r)
imf.k(r)
mf.cf(d)
mf.h(d)
mf.k(d)
pull.chr(cross, chr)
read.cross.csv(dir, file, sep=",", na.strings="-",
genotypes=c("A","H","B","C","D"),
estimate.map=TRUE)
read.cross.gary(dir, genfile, mnamesfile, chridfile, phefile,
pnamesfile, mapfile)
read.cross.karl(dir, genfile, mapfile, phefile)
read.cross.mm(dir, rawfile, mapfile, estimate.map)
ripple.perm1(n)
ripple.perm2(n)
ripple.perm.sub(x, mat)
scanone.perm(cross, pheno.col=1, model=c("normal","binary","2part","np"),
method=c("em","imp","hk","mr"), addcov=NULL, intcov=NULL,
upper=TRUE, ties.random=FALSE, start=NULL, maxit=4000,
tol=1e-4, n.perm=1000, trace=TRUE)
scantwo.perm(cross, pheno.col=1, method=c("em","imp","hk","mr"),
addcov=NULL, intcov=NULL, incl.markers=FALSE,
maxit=4000, tol=1e-4, trace=FALSE, n.perm=1000)
sim.cross.4way(map, model, n.ind, error.prob, missing.prob,
partial.missing.prob, keep.errorind, map.function)
sim.cross.bc(map, model, n.ind, error.prob, missing.prob,
keep.errorind, map.function)
sim.cross.f2(map, model, n.ind, error.prob, missing.prob,
partial.missing.prob, keep.errorind, map.function)
print.summary.cross(x, ...)
print.summary.ripple(x, ...)
print.summary.scanone(x, ...)
print.summary.scantwo(x, ...)
vbscan(cross, pheno.col=1, upper=FALSE, method="em",
maxit=4000, tol=1e-4)
write.cross.csv(cross, filestem="data", chr, digits=5)
write.cross.mm(cross, filestem="data", chr, digits=5)