reviseXdata(type=c("f2","bc","bcsft"), expandX=c("simple","standard","full"),
            sexpgm, geno, prob, draws, pairprob, cross.attr, force=FALSE)
calc.plod(lod, nterms, type=c("f2","bc"), penalties)
checkcovar(cross, pheno.col, addcovar, intcovar, perm.strata,
           ind.noqtl=NULL, weights=NULL, verbose=TRUE)
clean(object, ...)
condense(object)
convert(object, ...)
convert2bcsft(cross, BC.gen = 0, F.gen = 0, estimate.map = TRUE,
              error.prob=0.0001, map.function=c("haldane","kosambi","c-f","morgan"),
              verbose=FALSE)
create.map(map, step, off.end, stepwidth=c("fixed", "variable", "max"))
find.pseudomarkerpos(cross, marker, where=c("draws", "prob"))
flipcross(cross)
genAllPartitions(n.taxa, taxa)
getsex(cross)
addmarkerstointervalmap(cross,intervalresult,verbose=FALSE)
mqm_version()
scanall(cross, scanfunction=scanone, multicore=TRUE, n.clusters=1,
        batchsize=10, FF=0,cofactors=NULL, ..., plot=FALSE, verbose=FALSE)
getgenonames(type=c("f2","bc","riself","risib","4way","dh","haploid","special","bcsft"),
             chrtype=c("A","X"), expandX=c("simple","standard","full"),
             sexpgm, cross.attr)
imf.cf(r)
imf.h(r)
imf.k(r)
imf.m(r)
imf.stahl(r, m=0, p=0, tol=1e-12, maxit=1000)
locatemarker(map, pos, chr, flag)
## S3 method for class 'scantwocondensed'
max(object, lodcolumn=1,
    what=c("best", "full", "add", "int"),
    na.rm=TRUE, ...)
mf.cf(d)
mf.h(d)
mf.k(d)
mf.m(d)
mf.stahl(d, m=0, p=0)
polyplot(x, type='b', legend=TRUE,legendloc=0, labels=NULL, cex =
         par("cex"), pch = 19, gpch = 21, bg = par("bg"), color = par("fg"),
         col=NULL, ylim=range(x[is.finite(x)]), xlim = NULL, main = NULL, xlab =
         NULL, ylab = NULL, add=FALSE, ...)
## S3 method for class 'addcovarint'
print(x, ...)
## S3 method for class 'addint'
print(x, ...)
## S3 method for class 'compactqtl'
print(x, ...)
## S3 method for class 'summary.comparegeno'
print(x, ...)
## S3 method for class 'cross'
print(x, ...)
## S3 method for class 'map'
print(x, ...)
## S3 method for class 'qtl'
print(x, ...)
## S3 method for class 'scanoneboot'
print(x, ...)
## S3 method for class 'scantwo'
print(x, ...)
## S3 method for class 'summary.addpair'
print(x, ...)
## S3 method for class 'summary.compactqtl'
print(x, ...)
## S3 method for class 'summary.cross'
print(x, ...)
## S3 method for class 'summary.fitqtl'
print(x, ...)
## S3 method for class 'summary.map'
print(x, ...)
## S3 method for class 'summary.qtl'
print(x, ...)
## S3 method for class 'summary.ripple'
print(x, ...)
## S3 method for class 'summary.scanone'
print(x, ...)
## S3 method for class 'summary.scanoneperm'
print(x, ...)
## S3 method for class 'summary.scantwo'
print(x, ...)
## S3 method for class 'summary.scantwo.old'
print(x, ...)
## S3 method for class 'summary.scantwoperm'
print(x, ...)
replacemap(object, map)
subrousummaryscantwo(object, for.perm=FALSE)
## S3 method for class 'scantwocondensed'
summary(object, thresholds,
         what=c("best", "full", "add", "int"),
         perms, alphas, lodcolumn=1, pvalues=FALSE,
         allpairs=TRUE, ...)
## S3 method for class 'addcovarint'
summary(object, ...)
## S3 method for class 'addint'
summary(object, ...)
## S3 method for class 'compactqtl'
summary(object, ...)
checkStepwiseqtlStart(qtl, formula, covar=NULL)
checkformula(formula, qtl.name, covar.name)
countqtlterms(formula, ignore.covar=TRUE)
deparseQTLformula(formula, reorderterms=FALSE)
fitqtlengine(pheno, qtl, covar=NULL, formula, method=c("imp", "hk"),
         model=c("normal", "binary"),
         dropone=TRUE, get.ests=FALSE, run.checks=TRUE, cross.attr,
         crosstype, sexpgm, tol, maxit, forceXcovar=FALSE)
matchchr(selection, thechr)
parseformula(formula, qtl.dimname, covar.dimname)
reviseqtlnuminformula(formula, oldnum, newnum)