Index

A

addCovariates() (limmbo.io.input.InputData method) addGenotypes() (limmbo.io.input.InputData method) addPCs() (limmbo.io.input.InputData method)

addPhenotypes() (limmbo.io.input.InputData method) addRelatedness() (limmbo.io.input.InputData method) addVarianceComponents() (limmbo.io.input.InputData method)

B

boolanize() (in module limmbo.utils.utils)

C

combineBootstrap() (limmbo.core.vdbootstrap.LiMMBo method) commonSamples() (limmbo.io.input.InputData method)

computeEmpiricalP() (limmbo.core.gwas.GWAS method) computeFDR() (limmbo.core.gwas.GWAS method)

G

generate_permutation() (in module limmbo.utils.utils) getAlleleFrequencies() (limmbo.io.input.InputData method) getCovariates() (limmbo.io.reader.ReadData method) getEigen() (in module limmbo.utils.utils) getGenotypes() (limmbo.io.reader.ReadData method) getGWASargs() (in module limmbo.io.parser) getPCs() (limmbo.io.reader.ReadData method)

getPhenotypes() (limmbo.io.reader.ReadData method) getRelatedness() (limmbo.io.reader.ReadData method) getSampleSubset() (limmbo.io.reader.ReadData method) getTraitSubset() (limmbo.io.reader.ReadData method) getVariance() (in module limmbo.utils.utils) getVarianceComponents() (limmbo.io.reader.ReadData method) getVarianceEstimationArgs() (in module limmbo.io.parser) GWAS (class in limmbo.core.gwas)

I

inflate_matrix() (in module limmbo.utils.utils)

InputData (class in limmbo.io.input)

L

LiMMBo (class in limmbo.core.vdbootstrap) limmbo.core.gwas (module)

limmbo.io (module) limmbo.utils.utils (module)

M

manhattanQQ() (limmbo.core.gwas.GWAS method)

match() (in module limmbo.utils.utils)

N

nans() (in module limmbo.utils.utils)

R

ReadData (class in limmbo.io.reader) regress() (limmbo.io.input.InputData method)

regularize() (in module limmbo.utils.utils) runAssociationAnalysis() (limmbo.core.gwas.GWAS method) runBootstrapCovarianceEstimation() (limmbo.core.vdbootstrap.LiMMBo method)

S

saveAssociationResults() (limmbo.core.gwas.GWAS method) saveVarianceComponents() (limmbo.core.vdbootstrap.LiMMBo method)

scale() (in module limmbo.utils.utils) standardiseGenotypes() (limmbo.io.input.InputData method) subsetTraits() (limmbo.io.input.InputData method)

T

transform() (limmbo.io.input.InputData method)

V

vd_reml() (in module limmbo.core.vdsimple)

verboseprint() (in module limmbo.utils.utils)