Index

Symbols

--ancestry haptools-transform command line option, [1] --bp haptools-karyogram command line option, [1] --centromeres haptools-karyogram command line option, [1] --chroms haptools-simgenotype command line option, [1] --chunk-size haptools-ld command line option, [1] haptools-simphenotype command line option, [1] haptools-transform command line option, [1] --clump-chrom-field haptools-clump command line option, [1] --clump-field haptools-clump command line option, [1] --clump-id-field haptools-clump command line option, [1] --clump-kb haptools-clump command line option, [1] --clump-p1 haptools-clump command line option, [1] --clump-p2 haptools-clump command line option, [1] --clump-pos-field haptools-clump command line option, [1] --clump-r2 haptools-clump command line option, [1] --colors haptools-karyogram command line option, [1] --discard-missing haptools-ld command line option, [1] haptools-transform command line option, [1] --environment haptools-simphenotype command line option, [1] --from-gts haptools-ld command line option, [1] --gts-snps haptools-clump command line option, [1] --gts-strs haptools-clump command line option, [1] --heritability haptools-simphenotype command line option, [1] --id haptools-ld command line option, [1] haptools-simphenotype command line option, [1] haptools-transform command line option, [1] --ids-file haptools-ld command line option, [1] haptools-simphenotype command line option, [1] haptools-transform command line option, [1] --ld haptools-clump command line option, [1] --mapdir haptools-simgenotype command line option, [1] --model haptools-simgenotype command line option, [1] --no-normalize haptools-simphenotype command line option, [1] --no-sort haptools-index command line option, [1] --no_replacement haptools-simgenotype command line option, [1] --normalize haptools-simphenotype command line option, [1] --only_breakpoint haptools-simgenotype command line option, [1] --out haptools-clump command line option, [1] haptools-karyogram command line option, [1] haptools-simgenotype command line option, [1] --output haptools-index command line option, [1] haptools-ld command line option, [1] haptools-simphenotype command line option, [1] haptools-transform command line option, [1] --pop_field haptools-simgenotype command line option, [1] --prevalence haptools-simphenotype command line option, [1] --ref_vcf haptools-simgenotype command line option, [1]

--region haptools-ld command line option, [1] haptools-simgenotype command line option, [1] haptools-simphenotype command line option, [1] haptools-transform command line option, [1] --repeats haptools-simphenotype command line option, [1] --replications haptools-simphenotype command line option, [1] --sample haptools-karyogram command line option, [1] haptools-ld command line option, [1] haptools-simphenotype command line option, [1] haptools-transform command line option, [1] --sample_field haptools-simgenotype command line option, [1] --sample_info haptools-simgenotype command line option, [1] --samples-file haptools-ld command line option, [1] haptools-simphenotype command line option, [1] haptools-transform command line option, [1] --seed haptools-simgenotype command line option, [1] haptools-simphenotype command line option, [1] --sort haptools-index command line option, [1] --summstats-snps haptools-clump command line option, [1] --summstats-strs haptools-clump command line option, [1] --title haptools-karyogram command line option, [1] --verbosity haptools-clump command line option, [1] haptools-index command line option, [1] haptools-karyogram command line option, [1] haptools-ld command line option, [1] haptools-simgenotype command line option, [1] haptools-simphenotype command line option, [1] haptools-transform command line option, [1] --version haptools command line option, [1], [2], [3], [4], [5], [6], [7] -c haptools-ld command line option, [1] haptools-simphenotype command line option, [1] haptools-transform command line option, [1] -h haptools-simphenotype command line option, [1] -I haptools-ld command line option, [1] haptools-simphenotype command line option, [1] haptools-transform command line option, [1] -i haptools-ld command line option, [1] haptools-simphenotype command line option, [1] haptools-transform command line option, [1] -o haptools-index command line option, [1] haptools-ld command line option, [1] haptools-simphenotype command line option, [1] haptools-transform command line option, [1] -p haptools-simphenotype command line option, [1] -r haptools-simphenotype command line option, [1] -S haptools-ld command line option, [1] haptools-simphenotype command line option, [1] haptools-transform command line option, [1] -s haptools-ld command line option, [1] haptools-simphenotype command line option, [1] haptools-transform command line option, [1] -v haptools-clump command line option, [1] haptools-index command line option, [1] haptools-karyogram command line option, [1] haptools-ld command line option, [1] haptools-simgenotype command line option, [1] haptools-simphenotype command line option, [1] haptools-transform command line option, [1]

_

__iter__() (haptools.data.genotypes.Genotypes method) (haptools.data.genotypes.GenotypesPLINK method) (haptools.data.haplotypes.Haplotypes method) (haptools.data.phenotypes.Phenotypes method)

A

allele (haptools.data.haplotypes.Variant attribute) ancestry (haptools.transform.HaplotypeAncestry attribute)

append() (haptools.data.phenotypes.Phenotypes method) append_suffix() (in module haptools.index)

B

beta (haptools.sim_phenotype.Effect attribute) (haptools.sim_phenotype.Haplotype attribute) (haptools.sim_phenotype.Repeat attribute)

Breakpoints (class in haptools.data.breakpoints)

C

calc_ld() (in module haptools.ld) check_biallelic() (haptools.data.genotypes.Genotypes method) (haptools.data.genotypes.GenotypesPLINKTR method) (haptools.data.genotypes.GenotypesTR method) (haptools.transform.GenotypesAncestry method) check_header() (haptools.data.haplotypes.Haplotypes method) check_maf() (haptools.data.genotypes.Genotypes method) (haptools.data.genotypes.GenotypesPLINKTR method) (haptools.data.genotypes.GenotypesTR method) check_missing() (haptools.data.genotypes.Genotypes method) (haptools.data.phenotypes.Phenotypes method) (haptools.transform.GenotypesAncestry method)

check_phase() (haptools.data.genotypes.Genotypes method) check_sorted() (haptools.data.genotypes.Genotypes method) check_version() (haptools.data.haplotypes.Haplotypes method) chrom (haptools.data.haplotypes.Haplotype attribute) (haptools.data.haplotypes.Repeat attribute) classproperty (class in haptools.data.haplotypes) clumpstr() (in module haptools.clump) ComputeExactLD() (in module haptools.clump) ComputeLD() (in module haptools.clump) Covariates (class in haptools.data.covariates)

D

Data (class in haptools.data.data)

description (haptools.data.haplotypes.Extra attribute)

E

Effect (class in haptools.sim_phenotype) encode() (haptools.data.breakpoints.Breakpoints method) end (haptools.data.haplotypes.Haplotype attribute) (haptools.data.haplotypes.Repeat attribute) (haptools.data.haplotypes.Variant attribute) Extra (class in haptools.data.haplotypes)

extras_head() (haptools.data.haplotypes.Haplotype class method) (haptools.data.haplotypes.Repeat class method) (haptools.data.haplotypes.Variant class method) extras_order() (haptools.data.haplotypes.Haplotype class method) (haptools.data.haplotypes.Repeat class method) (haptools.data.haplotypes.Variant class method)

F

fmt (haptools.data.haplotypes.Extra attribute) fmt_str (haptools.data.haplotypes.Extra property) from_hap_spec() (haptools.data.haplotypes.Extra class method) (haptools.data.haplotypes.Haplotype class method) (haptools.data.haplotypes.Repeat class method) (haptools.data.haplotypes.Variant class method) (haptools.sim_phenotype.Effect class method)

G

GENOTYPES haptools-ld command line option, [1] haptools-simphenotype command line option, [1] haptools-transform command line option, [1] Genotypes (class in haptools.data.genotypes) GenotypesAncestry (class in haptools.transform) GenotypesPLINK (class in haptools.data.genotypes) GenotypesPLINKTR (class in haptools.data.genotypes) GenotypesTR (class in haptools.data.genotypes)

GenotypesVCF (class in haptools.data.genotypes) get_segment() (in module haptools.sim_genotype) GetCentromereClipMask() (in module haptools.karyogram) GetChrom() (in module haptools.karyogram) GetChromOrder() (in module haptools.karyogram) GetCmRange() (in module haptools.karyogram) GetHaplotypeBlocks() (in module haptools.karyogram) GetNextIndexVariant() (haptools.clump.SummaryStats method) GetOverlappingSamples() (in module haptools.clump) GetPopList() (in module haptools.karyogram)

H

Haplotype (class in haptools.data.haplotypes) (class in haptools.ld) (class in haptools.sim_phenotype) HaplotypeAncestry (class in haptools.transform) HAPLOTYPES haptools-index command line option, [1] haptools-ld command line option, [1] haptools-simphenotype command line option, [1] haptools-transform command line option, [1] Haplotypes (class in haptools.data.haplotypes) HaplotypesAncestry (class in haptools.transform) haptools command line option --version, [1], [2], [3], [4], [5], [6], [7] haptools-clump command line option --clump-chrom-field, [1] --clump-field, [1] --clump-id-field, [1] --clump-kb, [1] --clump-p1, [1] --clump-p2, [1] --clump-pos-field, [1] --clump-r2, [1] --gts-snps, [1] --gts-strs, [1] --ld, [1] --out, [1] --summstats-snps, [1] --summstats-strs, [1] --verbosity, [1] -v, [1] haptools-index command line option --no-sort, [1] --output, [1] --sort, [1] --verbosity, [1] -o, [1] -v, [1] HAPLOTYPES, [1] haptools-karyogram command line option --bp, [1] --centromeres, [1] --colors, [1] --out, [1] --sample, [1] --title, [1] --verbosity, [1] -v, [1] haptools-ld command line option --chunk-size, [1] --discard-missing, [1] --from-gts, [1] --id, [1] --ids-file, [1] --output, [1] --region, [1] --sample, [1] --samples-file, [1] --verbosity, [1] -c, [1] -i, [1] -I, [1] -o, [1] -s, [1] -S, [1] -v, [1] GENOTYPES, [1] HAPLOTYPES, [1] TARGET, [1] haptools-simgenotype command line option --chroms, [1] --mapdir, [1] --model, [1] --no_replacement, [1] --only_breakpoint, [1] --out, [1] --pop_field, [1] --ref_vcf, [1] --region, [1] --sample_field, [1] --sample_info, [1] --seed, [1] --verbosity, [1] -v, [1]

haptools-simphenotype command line option --chunk-size, [1] --environment, [1] --heritability, [1] --id, [1] --ids-file, [1] --no-normalize, [1] --normalize, [1] --output, [1] --prevalence, [1] --region, [1] --repeats, [1] --replications, [1] --sample, [1] --samples-file, [1] --seed, [1] --verbosity, [1] -c, [1] -h, [1] -i, [1] -I, [1] -o, [1] -p, [1] -r, [1] -s, [1] -S, [1] -v, [1] GENOTYPES, [1] HAPLOTYPES, [1] haptools-transform command line option --ancestry, [1] --chunk-size, [1] --discard-missing, [1] --id, [1] --ids-file, [1] --output, [1] --region, [1] --sample, [1] --samples-file, [1] --verbosity, [1] -c, [1] -i, [1] -I, [1] -o, [1] -s, [1] -S, [1] -v, [1] GENOTYPES, [1] HAPLOTYPES, [1] haptools.clump module haptools.data.breakpoints module haptools.data.covariates module haptools.data.data module haptools.data.genotypes module haptools.data.haplotypes module haptools.data.phenotypes module haptools.index module haptools.karyogram module haptools.ld module haptools.sim_genotype module haptools.sim_phenotype module haptools.transform module hook_compressed() (haptools.data.data.Data static method)

I

id (haptools.data.haplotypes.Haplotype attribute) ID (haptools.data.haplotypes.Haplotype property) id (haptools.data.haplotypes.Repeat attribute) ID (haptools.data.haplotypes.Repeat property) id (haptools.data.haplotypes.Variant attribute)

ID (haptools.data.haplotypes.Variant property) id (haptools.sim_phenotype.Effect attribute) index() (haptools.data.genotypes.Genotypes method) (haptools.data.haplotypes.Haplotypes method) (haptools.data.phenotypes.Phenotypes method) index_haps() (in module haptools.index)

L

ld (haptools.ld.Haplotype attribute) Load() (haptools.clump.SummaryStats method) load() (haptools.data.breakpoints.Breakpoints class method) (haptools.data.data.Data class method) (haptools.data.genotypes.Genotypes class method) (haptools.data.genotypes.GenotypesPLINKTR class method) (haptools.data.genotypes.GenotypesTR class method) (haptools.data.haplotypes.Haplotypes class method) (haptools.data.phenotypes.Phenotypes class method)

LoadVariant() (in module haptools.clump)

M

merge() (haptools.data.haplotypes.Haplotypes class method) merge_variants() (haptools.data.genotypes.Genotypes class method) (haptools.transform.GenotypesAncestry method) module haptools.clump haptools.data.breakpoints haptools.data.covariates haptools.data.data haptools.data.genotypes haptools.data.haplotypes haptools.data.phenotypes haptools.index haptools.karyogram haptools.ld haptools.sim_genotype haptools.sim_phenotype haptools.transform

N

name (haptools.data.haplotypes.Extra attribute)

normalize_gts() (haptools.sim_phenotype.PhenoSimulator method)

O

output_vcf() (in module haptools.sim_genotype)

P

pearson_corr_ld() (in module haptools.ld) PhenoSimulator (class in haptools.sim_phenotype) Phenotypes (class in haptools.data.phenotypes)

PlotHaplotypeBlock() (in module haptools.karyogram) PlotKaryogram() (in module haptools.karyogram) population_array() (haptools.data.breakpoints.Breakpoints method)

Q

QueryWindow() (haptools.clump.SummaryStats method)

R

read() (haptools.data.breakpoints.Breakpoints method) (haptools.data.data.Data method) (haptools.data.genotypes.Genotypes method) (haptools.data.genotypes.GenotypesPLINK method) (haptools.data.genotypes.GenotypesPLINKTR method) (haptools.data.haplotypes.Haplotypes method) (haptools.data.phenotypes.Phenotypes method) (haptools.transform.GenotypesAncestry method)

read_samples() (haptools.data.genotypes.GenotypesPLINK method) read_variants() (haptools.data.genotypes.GenotypesPLINK method) recode() (haptools.data.breakpoints.Breakpoints method) RemoveClump() (haptools.clump.SummaryStats method) Repeat (class in haptools.data.haplotypes) (class in haptools.sim_phenotype) run() (haptools.sim_phenotype.PhenoSimulator method)

S

simulate_gt() (in module haptools.sim_genotype) simulate_pt() (in module haptools.sim_phenotype) sort() (haptools.data.haplotypes.Haplotype method) (haptools.data.haplotypes.Haplotypes method) standardize() (haptools.data.phenotypes.Phenotypes method) start (haptools.data.haplotypes.Haplotype attribute) (haptools.data.haplotypes.Repeat attribute) (haptools.data.haplotypes.Variant attribute)

start_segment() (in module haptools.sim_genotype) subset() (haptools.data.genotypes.Genotypes method) (haptools.data.haplotypes.Haplotypes method) (haptools.data.phenotypes.Phenotypes method) (haptools.transform.GenotypesAncestry method) SummaryStats (class in haptools.clump)

T

TARGET haptools-ld command line option, [1] to_hap_spec() (haptools.data.haplotypes.Extra method) (haptools.data.haplotypes.Haplotype method) (haptools.data.haplotypes.Repeat method) (haptools.data.haplotypes.Variant method) to_str() (haptools.data.haplotypes.Haplotypes method) transform() (haptools.data.haplotypes.Haplotype method) (haptools.data.haplotypes.Haplotypes method) (haptools.transform.HaplotypeAncestry method) (haptools.transform.HaplotypesAncestry method)

transform_haps() (in module haptools.transform) TRRecordHarmonizerRegion (class in haptools.data.genotypes) types (haptools.data.haplotypes.Haplotype attribute) (haptools.data.haplotypes.Repeat attribute) (haptools.data.haplotypes.Variant attribute)

U

unset() (haptools.data.data.Data method)

V

validate_params() (in module haptools.sim_genotype) Variant (class in haptools.clump) (class in haptools.data.haplotypes)

variants (haptools.data.haplotypes.Haplotype attribute) varIDs (haptools.data.haplotypes.Haplotype property) version (haptools.data.haplotypes.Haplotypes attribute)

W

write() (haptools.data.breakpoints.Breakpoints method) (haptools.data.genotypes.GenotypesPLINK method) (haptools.data.genotypes.GenotypesPLINKTR method) (haptools.data.genotypes.GenotypesVCF method) (haptools.data.haplotypes.Haplotypes method) (haptools.data.phenotypes.Phenotypes method) (haptools.sim_phenotype.PhenoSimulator method) (haptools.transform.GenotypesAncestry method)

write_breakpoints() (in module haptools.sim_genotype) write_samples() (haptools.data.genotypes.GenotypesPLINK method) write_variants() (haptools.data.genotypes.GenotypesPLINK method) (haptools.data.genotypes.GenotypesPLINKTR method) WriteClump() (in module haptools.clump)