API for gkeele/miqtl
Suite of QTL Mapping Functions

Global functions
E.step Source code
ENV Source code
M.step Source code
allele.plotter.region Source code
allele.plotter.whole Man page Source code
apply.contrast Source code
assert.happy Source code
averaged.mi.parametric.bootstrap Source code
bayesian.bootstrap Source code
bayesian.bootstrap.deblup Source code
calc.LOD.drop Source code
calc.LRT.mean.coef Source code
calc.SIM.cache Source code
calc.dist.cache Source code
calc.dist.from.balance Source code
calc.kinship.from.genomecache.with.DOQTL Source code
calc.mi.LRT Source code
case.bootstrap Source code
caught.error Source code
check.for.lmer.formula Source code
check.l2.norm Source code
check.max.category Source code
ci.mean Source code
ci.median Source code
collapse.genomecache Man page Source code
condition.out.locus.for.scan Man page Source code
convert.DOQTL.to.HAPPY Man page Source code
convert.additive.DOQTL.array.to.HAPPY Source code
convert.full.DOQTL.array.to.HAPPY Man page Source code
convert.qtl2.to.HAPPY Man page Source code
convert.qtl2.to.HAPPY.with.map Source code
create.treatment.contrast.matrix Source code
dfapply Source code
double.averaged.mi.parametric.bootstrap Source code
elem Source code
extract.chr.max.statistics.from.genomewide Source code
extract.imputed.design.matrix.from.doqtl.genotype Source code
extract.mediation.qr Source code
extract.qr Man page Source code
extract.r2.interval Man page Source code
force.logical Source code
formula.as.string Source code
generate.qr.permutation.index.matrix Man page Source code
generate.sample.outcomes.matrix Man page Source code
generate.simple.permutation.index.matrix Source code
generate.simple.sample.outcomes.matrix Man page Source code
genome.plotter.chr Man page Source code
genome.plotter.region Man page Source code
genome.plotter.to.pdf Man page Source code
genome.plotter.whole Man page Source code
genotype.to.count Source code
genotype.to.factor Source code
genotype.to.hier Source code
get.SIM Source code
get.allele.effects.from.fixef Source code
get.allele.effects.from.fixef.eQTL Source code
get.allele.effects.from.ranef Source code
get.blup.from.ranef.fit Source code
get.coef.dif Source code
get.expanded.X Source code
get.expanded.y Source code
get.f.stat.p.val Source code
get.gev.padjust Source code
get.gev.thresholds Man page Source code
get.mixture.likelihood Source code
get.p.value Source code
get.reduced.threshold.from.F Source code
get.weights.from.diplotype.prob.data Source code
gls.fit Source code
grab.locus.from.scan Man page Source code
grab.max.pos.from.scan Source code
grab.max.statistic.from.scan Source code
grab.min.pos.from.scan Source code
happy.check.bp Source code
happy.clear.reserve Source code
happy.get.allele.freq Source code
happy.get.allowed.models Source code
happy.get.bp Source code
happy.get.chromosome Source code
happy.get.chromosome.length Source code
happy.get.design Source code
happy.get.design.old Source code
happy.get.diplotype.tensor Source code
happy.get.first.marker Source code
happy.get.genotype Source code
happy.get.interval.length Source code
happy.get.interval.midpoint Source code
happy.get.interval.over Source code
happy.get.interval.range Source code
happy.get.intervals Source code
happy.get.intervals.in.range Source code
happy.get.last.marker Source code
happy.get.location Source code
happy.get.markers Source code
happy.get.markers.between Source code
happy.get.models Source code
happy.get.next.marker Source code
happy.get.position Source code
happy.get.previous.marker Source code
happy.get.reserve.limit Source code
happy.get.reserved.marker Source code
happy.get.strains Source code
happy.get.subjects Source code
happy.has.chromosomes Source code
happy.has.markers Source code
happy.has.model Source code
happy.has.reserved.marker Source code
happy.has.subjects Source code
happy.init.reserve Source code
happy.is.auto.reserve Source code
happy.list.chromosomes Source code
happy.load.data Source code
happy.load.genome Source code
happy.load.marker Source code
happy.make.colnames Source code
happy.matrixop.diplotypes.to.full Source code
happy.matrixop.full.asymmetric.to.diplotypes Source code
happy.matrixop.full.to.diplotypes Source code
happy.num.strains Source code
happy.reserve.exists Source code
happy.reserve.get Source code
happy.reserve.has Source code
happy.reserve.has.scratch Source code
happy.reserve.marker Source code
happy.reserve.markers Source code
happy.reserve.memory.usage Source code
happy.reserve.put Source code
happy.set.auto.reserve Source code
ifow Source code
igrep Source code
imputed.snp.scan.h2lmm Man page Source code
incidence.matrix Source code
inspect.ci.genome.plotter.whole Source code
instability.lm.scan Man page Source code
interpolate Source code
interpolate.Sys.env Source code
invlogit Source code
is.formula Source code
is.wholenumber Source code
list.subdirs Source code
lmmbygls Man page Source code
lmmbygls.random Source code
lmmbygls.replicates Source code
lmmbylmer Source code
logit Source code
make.EM.alt.formula Source code
make.alt.formula Source code
make.augment.weights Source code
make.full.null.augment.K Source code
make.full.null.augment.data Source code
make.imputed.design.matrix.list.for.all.loci Source code
make.null.formula Source code
make.processed.data Source code
make.simple.augment.K Source code
make.simple.augment.data Source code
make.snp.alt.formula Source code
make.snp.null.formula Source code
map.eq Source code
mediation.scan.qr Source code
multi.imput.lmmbygls Source code
nonparametric.bootstrap Source code
nonparametric.bootstrap.deblup Source code
null.pvalue.ci.plot Source code
null.pvalue.plot Source code
object.sizes Source code
pairwise.cor.snp.scan Man page Source code
plot_SIM Source code
plot_dist Source code
polygon.with.nas Source code Source code
predict.lmmbygls Source code
prob.heatmap Man page Source code
prob.heatmap.from.matrix Source code
prob.image Source code
process.random.formula Source code
process_eigen_decomposition Source code
pvalue.per.locus.im Source code
reduce.large.K Source code
regress.out.average.qtl Source code
regress.out.qtl Source code
remove.weights Source code
remove.whitespace.formula Source code
replicates.eigen Source code
reshape.X Source code
rint Man page Source code
rotate.full.to.add.data Source code
run.imputation Source code
run.positional.scans Man page Source code
run.qr.permutation.threshold.mediation.scans Source code
run.qr.permutation.threshold.scans Man page Source code
run.simple.permutation.threshold.scans Man page Source code
run.threshold.scans Man page Source code
scan.EM Source code
scan.h2lmm Man page Source code
scan.h2lmm.deBLUP Source code
scan.qr Man page Source code
se.mean Source code
sim.instability.lm.scan Source code
simulate.from.average.over.imputations Source code
single.chr.plotter.w.ci Man page Source code
snp.genome.plotter.w.r2 Man page Source code
snp.genome.plotter.whole Man page Source code
snp.null.par.bs.threshold.scan Source code
snp.par.perm.threshold.scan Source code
snp.perm.threshold.scan Source code
split.formula Source code
split.pathname Source code
straineff.mapping.matrix Source code
strcat Source code
string.trim Source code
subsample.ci Source code
tr Source code
write.delim Source code
gkeele/miqtl documentation built on Nov. 19, 2017, 5:47 a.m.