R: Internal qtl functions

qtl-internal {qtl} | R Documentation

## Internal qtl functions

### Description

Internal qtl functions. These are generally not to be called by the user.

### 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)
    ## 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 '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,
             sexpgm, tol, maxit, forceXcovar=FALSE)
    matchchr(selection, thechr)
    parseformula(formula, qtl.dimname, covar.dimname)
    reviseqtlnuminformula(formula, oldnum, newnum)

### Author(s)

Karl W Broman, kbroman@biostat.wisc.edu

[Package qtl version 1.41-6 Index]