qtl-internal {qtl}R Documentation

Internal qtl functions

Description

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

Usage

adjust.rf.ri(r, type=c("self","sib"), chrtype=c("A","X"), expand=TRUE)
asnumericwithdec(x, dec=".")
calc.genoprob.special(cross, error.prob=0.0001,
                      map.function=c("haldane","kosambi","c-f","morgan"))
calc.pairprob(cross, step=0, off.end=0, error.prob=0.0001, 
              map.function=c("haldane","kosambi","c-f","morgan"), map,
              assumeCondIndep=FALSE)
calc.plod(lod, nterms, type=c("f2","bc"), penalties)
calcPermPval(peaks, perms)
charround(x, digits=1)
checkPhyloCrosses(crosses, taxa, nostop=FALSE)
checkPhyloPartition(partition, taxa)
checkcovar(cross, pheno.col, addcovar, intcovar, perm.strata, ind.noqtl=NULL, verbose=TRUE)
checkformula(formula, qtl.name, covar.name)
checkStepwiseqtlStart(qtl, formula, covar=NULL)
clean(object, ...)
condense(object)
convert(object, ...)
convertMWril(cross, parents, error.prob=0)
countqtlterms(formula, ignore.covar=TRUE)
create.map(map, step, off.end, stepwidth=c("fixed", "variable", "max"))
deparseQTLformula(formula, reorderterms=FALSE)
discan(cross, pheno, method=c("em","hk","mr"),
       addcovar=NULL, intcovar=NULL, maxit=4000, tol=1e-4,
       verbose=FALSE, give.warnings=TRUE, ind.noqtl)
dropfromqtlformula(formula, qtlnum)
dropXcol(type=c("f2","bc", "riself", "risib", "4way", "dh", "special"), sexpgm, cross.attr)
effectplot.getmark(cross, mname)
effectplot.calmeanse(pheno, mark1, mark2, geno1, geno2, ndraws, var.flag=c("pooled", "group"))
expandf2covar(thecovar)
find.pseudomarkerpos(cross, marker, where=c("draws", "prob"))
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)
fitstahl.estp(cross, error.prob=0.0001, m=0, tol=1e-4, maxit=4000)
fitstahl.estp.sub(p, cross, error.prob=0.0001, m=0, thetol=1e-4, maxit=4000)
fitstahl.este(cross, m=0, p=0, tol=1e-4, maxit=4000)
fitstahl.este.sub(error.prob, cross, m=0, p=0, thetol=1e-4, maxit=4000)
fitstahl.estpe(cross, m=0, tol=1e-4, maxit=4000)
fitstahl.estpe.sub(x, cross, m=0, thetol=1e-4, maxit=4000)
fixX4write(geno,sex,pgm,crosstype)
fixXgeno.bc(cross)
fixXgeno.f2(cross, alleles)
flipcross(cross)
markerforwsel(x, y, maxsize=7)
markerforwself2(x, y, maxsize=7)
genAllPartitions(n.taxa, taxa)
genotab.em(dat, tol=1e-6, maxit=10000, verbose=FALSE)
getsex(cross)

addmarkerstointervalmap(cross,intervalresult,verbose=FALSE)
calculatedensity(cross,distance=30)
checkdistances(cross,cofactors,dist=5)
circlelocations(nt)
drawcirculargenome(result,lodmarkers=FALSE,spacing=50)
drawspline(cn1, cn2, lwd = 1,col="blue",...)
estimatemarkerlod(interresults)
getChr(x)
getchromosomelength(result, chr)
getgenomelength(result)
locationtocircle(result, chr, loc, spacing=50, fixoutofbounds=TRUE, verbose=FALSE)
loopthroughmulti(cross,result,save=FALSE,spacing=100)
mqmextractpseudomarkers(mqmresult)
mqm_version()
scanall(cross, scanfunction=scanone, multicore=TRUE, n.clusters=1, batchsize=10, FF=0,cofactors=NULL, ..., plot=FALSE, verbose=FALSE)
scoremissingmarkers(cross)
stepsize(mqmpseudomarkers)

getgenonames(type=c("f2","bc","riself","risib","4way","dh","special"),
             chrtype=c("A","X"), expandX=c("simple","standard","full"),
             sexpgm, cross.attr)
getThird(x)
grab.arg.names(...)
imf.cf(r)
imf.h(r)
imf.k(r)
imf.m(r)
imf.stahl(r, m=0, p=0, tol=1e-12, maxit=1000)
interpmap(oldmap, newmap)
interpmap4scantwo(output, newmap)
LikePheVector(pheno, n.ind, n.phe)
locatemarker(map, pos, chr, flag)
makeSSmap(cross)
markerloglik(cross, marker, error.prob=0.0001)
matchchr(selection, thechr)
## S3 method for class 'scantwocondensed'
max(object, lodcolumn=1,
    what=c("best", "full", "add", "int"),
    df=FALSE, na.rm=TRUE, ...)
mf.cf(d)
mf.h(d)
mf.k(d)
mf.m(d)
mf.stahl(d, m=0, p=0)
mybinaryrep(n)
orderMarkers.sub(cross, chr, window=7, use.ripple=TRUE, verbose=FALSE)
ourline()
ourstop(...)
parseformula(formula, qtl.dimname, covar.dimname)
## S3 method for class 'effectscan'
plot(x, gap=25, ylim, mtick=c("line","triangle"),
     add.legend=TRUE, alternate.chrid=FALSE, ...)
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, ...)
printQTLformulanicely(formula, header, width, width2, sep=" ")
qtlByPartition(crosses, partition)
qtlformulasymmetric(formula, qtlnum1, qtlnum2)
read.cro.qtlcart(file)
read.cross.csv(dir, file, na.strings=c("-","NA"),
               genotypes=c("A","H","B","D","C"),
               estimate.map=TRUE, rotate=FALSE, ...)
read.cross.csvs(dir, genfile, phefile, na.strings=c("-","NA"),
                genotypes=c("A","H","B","D","C"),
                estimate.map=TRUE, rotate=FALSE, ...)
read.cross.gary(dir, genfile, mnamesfile, chridfile, phefile,
                pnamesfile, mapfile,estimate.map,na.strings)
read.cross.karl(dir, genfile, mapfile, phefile)
read.cross.mm(dir, rawfile, mapfile, estimate.map=TRUE)
read.cross.qtlcart(dir, crofile, mapfile)
read.cross.qtx(dir, file, estimate.map=TRUE)
read.map.qtlcart(file)
read.maps.mm(mapsfile)
reorgRIargmax(cross)
reorgRIdraws(cross)
reorgRIgenoprob(cross)
reorgRIpairprob(cross, pairprob)
replacemap(object, map)
revisecovar(sexpgm, covar)
reviseqtlnuminformula(formula, oldnum, newnum)
revisescantwodf(df)
reviseXdata(type=c("f2","bc"), expandX=c("simple","standard","full"),
            sexpgm, geno, prob, draws, pairprob, cross.attr, force=FALSE)
ripple.perm1(n)
ripple.perm2(n)
ripple.perm.sub(x, mat)
rippleSnowLik(orders, cross, error.prob, map.function, maxit, tol, sex.sp)
rippleSnowCountxo(orders, genodat, func)
roundqtlpos(x, digits = 1)
scanone.perm(cross, pheno.col=1, model=c("normal","binary","2part","np"),
             method=c("em","imp","hk","ehk","mr","mr-imp","mr-argmax"),
             addcovar=NULL, intcovar=NULL, weights=NULL,
             use=c("all.obs", "complete.obs"), upper=FALSE,
             ties.random=FALSE, start=NULL, maxit=4000,
             tol=1e-4, n.perm=1000, perm.Xsp=FALSE, perm.strata=NULL,
             verbose=TRUE, batchsize=250)
scanone.perm.engine(n.perm, cross, pheno.col, model,
                    method, addcovar, intcovar, weights, use,
                    upper, ties.random, start, maxit, tol,
                    verbose, perm.strata, batchsize=250)
scanoneXnull(type, sexpgm)
scantwo.perm(cross, pheno.col=1, model=c("normal","binary"),
             method=c("em","imp","hk","mr","mr-imp","mr-argmax"),
             addcovar=NULL, intcovar=NULL, weights=NULL,
             use=c("all.obs", "complete.obs"),
             incl.markers=FALSE, clean.output=FALSE, 
             clean.nmar=1, clean.distance=0,
             maxit=4000, tol=1e-4, verbose=FALSE,
             n.perm=1000, perm.strata, assumeCondIndep=FALSE,
             batchsize=250)
scantwo.perm.engine(n.perm, cross, pheno.col, model,
                    method, addcovar, intcovar, weights, use,
                    incl.markers, clean.output,  
                    clean.nmar=1, clean.distance=0,
                    maxit, tol, verbose,
                    perm.strata, assumeCondIndep=FALSE,
                    batchsize=250)
scantwoperm2scanoneperm(scantwoperms)
sim.bcg(n.ind, map, m, p,
        map.function=c("haldane","kosambi","c-f","morgan"))
sim.cross.4way(map, model, n.ind, error.prob, missing.prob,
               partial.missing.prob, keep.errorind, m, p, map.function)
sim.cross.bc(map, model, n.ind, error.prob, missing.prob,
             keep.errorind, m, p, map.function)
sim.cross.f2(map, model, n.ind, error.prob, missing.prob,
             partial.missing.prob, keep.errorind, m, p, map.function)
sim.ril(map, n.ril=1, type=c("sibmating", "selfing"), n.str=c("2","4","8"),
        m=0, p=0, error.prob=0, missing.prob=0, random.cross=TRUE)
snowCoreALL(x, all.data, scanfunction, cofactors, verbose=FALSE, ...)
snowCoreBOOT(x, all.data, scanfunction, bootmethod, cofactors, verbose=FALSE, ...)
sortPhyloPartitions(partitions, taxa)
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,
         df=FALSE, allpairs=TRUE, ...)
## S3 method for class 'addcovarint'
summary(object, ...)
## S3 method for class 'addint'
summary(object, ...)
## S3 method for class 'compactqtl'
summary(object, ...)
testchr(selection, thechr)
vbscan(cross, pheno.col=1, upper=FALSE, method="em", maxit=4000,
       tol=1e-4)
write.cross.csv(cross, filestem="data", digits=NULL, rotate=FALSE,
                split=FALSE)
write.cross.gary(cross, digits=NULL)
write.cross.mm(cross, filestem="data", digits=NULL)
write.cross.qtlcart(cross, filestem="data")

Author(s)

Karl W Broman, kbroman@biostat.wisc.edu


[Package qtl version 1.21-2 Index]