Usage
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)
"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, ...)
"print"(x, ...)
"print"(x, ...)
"print"(x, ...)
"print"(x, ...)
"print"(x, ...)
"print"(x, ...)
"print"(x, ...)
"print"(x, ...)
"print"(x, ...)
"print"(x, ...)
"print"(x, ...)
"print"(x, ...)
"print"(x, ...)
"print"(x, ...)
"print"(x, ...)
"print"(x, ...)
"print"(x, ...)
"print"(x, ...)
"print"(x, ...)
"print"(x, ...)
replacemap(object, map)
subrousummaryscantwo(object, for.perm=FALSE)
"summary"(object, thresholds, what=c("best", "full", "add", "int"), perms, alphas, lodcolumn=1, pvalues=FALSE, allpairs=TRUE, ...)
"summary"(object, ...)
"summary"(object, ...)
"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, sexpgm, tol, maxit, forceXcovar=FALSE)
matchchr(selection, thechr)
parseformula(formula, qtl.dimname, covar.dimname)
reviseqtlnuminformula(formula, oldnum, newnum)