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 |
build.position.scaffold | 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.manual.mark.locus | 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 |
expand.for.polygon | Source code |
extract.chr.max.statistics.from.genomewide | Man page Source code |
extract.imputed.design.matrix.from.doqtl.genotype | Source code |
extract.mediation.expression.qr | Man page Source code |
extract.mediation.qr | Man page 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.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.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 |
make_genotype_matrix | Source code |
map.eq | Source code |
mediation.scan.qr | Man page 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.ci | Source code |
plot_SIM | Source code |
plot_dist | Source code |
plot_locus.effect.from.scan | Man page Source code |
polygon.with.nas | Source code |
predict.lmmbygls | Source code |
prob.heatmap | Man page Source code |
prob.heatmap.from.matrix | Source code |
process.random.formula | Source code |
process_eigen_decomposition | Source code |
pvalue.per.locus.im | Source code |
rankZ | 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.expression.scans | Man page Source code |
run.qr.permutation.threshold.mediation.scans | Man page 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 |
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