Index

A

accession (core.lib.catalogapi.CatalogQuery property) (core.lib.models.ScoreVariant attribute) add_missing_positions_to_lists() (in module calc.lib.cache.targetvariants) ADDITIVE (core.lib.effecttype.EffectType attribute) adjust() (calc.lib.legacy.polygenicscore.AggregatedPGS method) AdjustArguments (class in calc.lib.legacy.polygenicscore) AdjustResults (class in calc.lib.legacy.polygenicscore) AggregatedPGS (class in calc.lib.legacy.polygenicscore) Allele (class in core.lib.models)

allele (core.lib.models.Allele attribute) allelefrequency_effect (core.lib.models.CatalogScoreVariant attribute) alleles_must_parse() (core.lib.models.CatalogScoreVariant class method) alt (match.lib.targetvariants.TargetVariant attribute) alts (calc.lib.cache.zarrmodels.ZarrVariantMetadata attribute) APOE_ALLELE (core.lib.models.VariantType attribute) arrowpaths (match.lib.scoringfileframe.ScoringFileFrame attribute) (match.lib.variantframe.VariantFrame attribute) average() (calc.lib.legacy.polygenicscore.PolygenicScore method)

B

BasePGSException BGEN (calc.lib.cache.genomefiletypes.GenomeFileType attribute)

BIM (match.lib.targetvariants.TargetType attribute) BuildError

C

cache_dir (calc.lib.cache.targetgenome.TargetGenome property) cache_variants() (calc.lib.cache.targetgenome.TargetGenome method) cached_positions (calc.lib.cache.targetgenome.TargetGenome property) calc module calc.lib module calc.lib.cache module calc.lib.cache.genomefiletypes module calc.lib.cache.targetgenome module calc.lib.cache.targetvariants module calc.lib.cache.zarrmodels module calc.lib.config module calc.lib.constants module calc.lib.legacy module calc.lib.legacy.polygenicscore module calc.lib.legacy.principalcomponents module calc.lib.score module calc.lib.score.scorepipeline module calc.lib.scorefile module calc.lib.types module calculate_scores() (calc.lib.score.scorepipeline.ScorePipeline method) CatalogCategory (class in core.lib.catalogapi) CatalogError CatalogQuery (class in core.lib.catalogapi) CatalogScoreHeader (class in core.lib.models) CatalogScoreVariant (class in core.lib.models) category (core.lib.catalogapi.CatalogQuery attribute)

check_complex_variants() (core.lib.models.CatalogScoreVariant method) check_effect_weights() (core.lib.models.CatalogScoreVariant method) check_even_length() (calc.lib.cache.zarrmodels.ZarrVariantMetadata method) check_extra_fields() (core.lib.models.CatalogScoreVariant method) check_format_version() (core.lib.models.CatalogScoreHeader class method) check_pgp_id() (core.lib.models.CatalogScoreHeader class method) check_pgs_id() (core.lib.models.CatalogScoreHeader class method) check_position() (core.lib.models.CatalogScoreVariant method) chr_name (calc.lib.cache.zarrmodels.ZarrVariantMetadata attribute) (core.lib.models.CatalogScoreVariant attribute) chr_pos (calc.lib.cache.zarrmodels.ZarrVariantMetadata attribute) chr_position (core.lib.models.CatalogScoreVariant attribute) chrom (calc.lib.cache.targetgenome.TargetGenome property) (match.lib.scoringfileframe.ScoringFileFrame attribute) (match.lib.targetvariants.TargetVariant attribute) (match.lib.targetvariants.TargetVariants property) (match.lib.variantframe.VariantFrame attribute) citation (core.lib.models.CatalogScoreHeader attribute) code_map (core.lib.pgsexceptions.ExceptionExitCodeMap attribute) collect() (match.lib.matchresult.MatchResult method) column_types (calc.lib.scorefile.Scorefiles attribute) CombineError compatible_effect_type (core.lib.models.ScoreLog attribute) complex_columns (core.lib.models.CatalogScoreVariant attribute) Config (class in calc.lib.config) config (in module calc.lib.config) core module core.lib module core.lib.catalogapi module core.lib.effecttype module core.lib.genomebuild module core.lib.models module core.lib.pgsexceptions module core.lib.scorefiles module CYP_ALLELE (core.lib.models.VariantType attribute)

D

dataset (calc.lib.legacy.principalcomponents.PrincipalComponents attribute) (match.lib.matchresult.MatchResult attribute) (match.lib.matchresult.MatchResults attribute) (match.lib.variantframe.VariantFrame attribute) db_path (calc.lib.score.scorepipeline.ScorePipeline property) df (calc.lib.legacy.polygenicscore.AggregatedPGS property) (calc.lib.legacy.polygenicscore.PolygenicScore property) (calc.lib.legacy.principalcomponents.PrincipalComponents property) (match.lib.matchresult.MatchResult attribute) (match.lib.matchresult.MatchResults property)

DOMINANT (core.lib.effecttype.EffectType attribute) dosage_0_weight (core.lib.models.CatalogScoreVariant attribute) dosage_1_weight (core.lib.models.CatalogScoreVariant attribute) dosage_2_weight (core.lib.models.CatalogScoreVariant attribute) download() (core.lib.scorefiles.ScoringFile method) DuplicateMatchError

E

effect_allele (core.lib.models.CatalogScoreVariant attribute) effect_type (core.lib.models.CatalogScoreVariant property) effect_weight (core.lib.models.CatalogScoreVariant attribute) effect_weight_must_float() (core.lib.models.CatalogScoreVariant class method) EffectType (class in core.lib.effecttype) EffectTypeError

elements (core.lib.scorefiles.ScoringFiles property) empty_string_to_none() (core.lib.models.CatalogScoreVariant class method) ExceptionExitCodeMap (class in core.lib.pgsexceptions) export_full_match_log() (calc.lib.score.scorepipeline.ScorePipeline method) export_scores() (calc.lib.score.scorepipeline.ScorePipeline method) export_summary_match_log() (calc.lib.score.scorepipeline.ScorePipeline method)

F

filename (calc.lib.cache.targetgenome.TargetGenome property) filetype (calc.lib.cache.targetgenome.TargetGenome property) filter() (match.lib.matchresult.MatchResults method) filter_summary (match.lib.matchresult.MatchResults property) filtered_matches (match.lib.matchresult.MatchResults property) format_version (core.lib.models.CatalogScoreHeader attribute) from_ipc() (match.lib.matchresult.MatchResult class method)

from_path() (core.lib.models.ScoreHeader class method) from_query() (core.lib.catalogapi.ScoreQueryResult class method) from_string() (core.lib.genomebuild.GenomeBuild class method) ftp_grch37_url (core.lib.catalogapi.ScoreQueryResult attribute) ftp_grch38_url (core.lib.catalogapi.ScoreQueryResult attribute) ftp_url (core.lib.catalogapi.ScoreQueryResult attribute) full_variant_log() (match.lib.matchresult.MatchResults method)

G

genome_build (core.lib.models.ScoreHeader attribute) (core.lib.scorefiles.ScoringFile property) GenomeBuild (class in core.lib.genomebuild) GenomeFileType (class in calc.lib.cache.genomefiletypes) GenomesNotFound genotypes (calc.lib.cache.targetvariants.TargetVariants property) genotypes_root (calc.lib.score.scorepipeline.ScorePipeline property)

genotypes_root_path (calc.lib.score.scorepipeline.ScorePipeline property) get_download_url() (core.lib.catalogapi.ScoreQueryResult method) get_position_df() (in module calc.lib.scorefile) get_query_url() (core.lib.catalogapi.CatalogQuery method) get_unique_positions() (calc.lib.scorefile.Scorefiles method) get_variants_from_zarr() (in module calc.lib.score.scorepipeline) GRCh37 (core.lib.genomebuild.GenomeBuild attribute) GRCh38 (core.lib.genomebuild.GenomeBuild attribute)

H

handle_uncaught_exception() (in module core.lib.pgsexceptions) harmonised_columns (core.lib.models.CatalogScoreVariant attribute) has_complex_alleles (core.lib.models.ScoreLog property) has_multiple_alleles (core.lib.models.Allele property) header (core.lib.models.ScoreLog attribute) (core.lib.scorefiles.ScoringFile property) HLA_AA (core.lib.models.VariantType attribute) HLA_ALLELE (core.lib.models.VariantType attribute) HLA_SEROTYPE (core.lib.models.VariantType attribute) hm_chr (core.lib.models.CatalogScoreVariant attribute) hm_inferOtherAllele (core.lib.models.CatalogScoreVariant attribute)

hm_match_chr (core.lib.models.CatalogScoreVariant attribute) hm_match_pos (core.lib.models.CatalogScoreVariant attribute) hm_pos (core.lib.models.CatalogScoreVariant attribute) hm_rsID (core.lib.models.CatalogScoreVariant attribute) hm_source (core.lib.models.CatalogScoreVariant attribute) (core.lib.models.VariantLog attribute) HmPOS_build (core.lib.models.CatalogScoreHeader attribute) HmPOS_date (core.lib.models.CatalogScoreHeader attribute) HmPOS_match_chr (core.lib.models.CatalogScoreHeader attribute) HmPOS_match_pos (core.lib.models.CatalogScoreHeader attribute) HR (core.lib.models.CatalogScoreVariant attribute)

I

id (match.lib.targetvariants.TargetVariant attribute) imputation_method (core.lib.models.CatalogScoreVariant attribute) inclusion_criteria (core.lib.models.CatalogScoreVariant attribute) infer_category() (core.lib.catalogapi.CatalogQuery method) InvalidAccessionError ipc_path (match.lib.matchresult.MatchResult attribute) is_complex (core.lib.models.CatalogScoreVariant property) (core.lib.models.VariantLog attribute) is_diplotype (core.lib.models.CatalogScoreVariant attribute) is_dominant (core.lib.models.CatalogScoreVariant attribute) is_duplicated (core.lib.models.ScoreVariant attribute) is_haplotype (core.lib.models.CatalogScoreVariant attribute)

is_harmonised (core.lib.models.CatalogScoreHeader property) (core.lib.models.CatalogScoreVariant property) (core.lib.models.ScoreHeader property) (core.lib.models.ScoreLog property) (core.lib.scorefiles.ScoringFile property) is_hm_bad (core.lib.models.CatalogScoreVariant property) is_interaction (core.lib.models.CatalogScoreVariant attribute) is_non_additive (core.lib.models.CatalogScoreVariant property) is_recessive (core.lib.models.CatalogScoreVariant attribute) is_snp (core.lib.models.Allele property) is_valid_allele() (in module calc.lib.cache.zarrmodels) is_wide (core.lib.scorefiles.ScoringFile property)

L

label() (match.lib.matchresult.MatchResults method) license (core.lib.catalogapi.ScoreQueryResult attribute) (core.lib.models.CatalogScoreHeader attribute) LiftoverError load_scores() (calc.lib.score.scorepipeline.ScorePipeline method) load_scoring_files() (in module calc.lib.scorefile) locus_name (core.lib.models.CatalogScoreVariant attribute) logger (in module calc.lib.cache.targetgenome) (in module calc.lib.cache.targetvariants) (in module calc.lib.cache.zarrmodels) (in module calc.lib.legacy.polygenicscore) (in module calc.lib.legacy.principalcomponents) (in module calc.lib.score.scorepipeline) (in module calc.lib.scorefile) (in module core.lib.catalogapi) (in module core.lib.scorefiles) (in module match.lib.matchresult) (in module match.lib.plinkscorefiles) (in module match.lib.scoringfileframe) (in module match.lib.variantframe)

M

match module match.lib module match.lib.matchresult module match.lib.normalisedscoringfile module match.lib.plinkscorefiles module match.lib.scoringfileframe module match.lib.targetvariants module match.lib.variantframe module match_candidates (match.lib.matchresult.MatchResults property) match_variants() (calc.lib.score.scorepipeline.ScorePipeline method) (in module match.lib.scoringfileframe) MatchError MatchRateError MatchResult (class in match.lib.matchresult) MatchResults (class in match.lib.matchresult) MatchValueError max_pcs (calc.lib.legacy.principalcomponents.PrincipalComponents property) melt() (calc.lib.legacy.polygenicscore.PolygenicScore method) merge() (calc.lib.cache.zarrmodels.ZarrVariantMetadata method) (match.lib.plinkscorefiles.PlinkScoreFiles method) method_compare (calc.lib.legacy.polygenicscore.AdjustArguments attribute) method_normalization (calc.lib.legacy.polygenicscore.AdjustArguments attribute) MISSING_GENOTYPE_SENTINEL_VALUE (in module calc.lib.constants) MISSING_GENOTYPE_TUPLE (in module calc.lib.constants) model_config (core.lib.models.CatalogScoreVariant attribute) (core.lib.models.ScoreLog attribute) (core.lib.models.ScoreVariant attribute)

model_meta (calc.lib.legacy.polygenicscore.AdjustResults attribute) models (calc.lib.legacy.polygenicscore.AdjustResults attribute) module calc calc.lib calc.lib.cache calc.lib.cache.genomefiletypes calc.lib.cache.targetgenome calc.lib.cache.targetvariants calc.lib.cache.zarrmodels calc.lib.config calc.lib.constants calc.lib.legacy calc.lib.legacy.polygenicscore calc.lib.legacy.principalcomponents calc.lib.score calc.lib.score.scorepipeline calc.lib.scorefile calc.lib.types core core.lib core.lib.catalogapi core.lib.effecttype core.lib.genomebuild core.lib.models core.lib.pgsexceptions core.lib.scorefiles match match.lib match.lib.matchresult match.lib.normalisedscoringfile match.lib.plinkscorefiles match.lib.scoringfileframe match.lib.targetvariants match.lib.variantframe

N

n_actual_variants (core.lib.models.ScoreLog property) NCBI35 (core.lib.genomebuild.GenomeBuild attribute) NCBI36 (core.lib.genomebuild.GenomeBuild attribute) non_additive_columns (core.lib.models.CatalogScoreVariant attribute) NONADDITIVE (core.lib.effecttype.EffectType attribute)

normalise() (core.lib.scorefiles.ScoringFile method) NormalisedScoringFile (class in match.lib.normalisedscoringfile) npcs_norm (calc.lib.legacy.principalcomponents.PrincipalComponents property) npcs_popcomp (calc.lib.legacy.principalcomponents.PrincipalComponents property) NUMPY_STRING_DTYPE (in module calc.lib.constants)

O

OR (core.lib.models.CatalogScoreVariant attribute) other_allele (core.lib.models.CatalogScoreVariant attribute)

out_dir (calc.lib.score.scorepipeline.ScorePipeline property) output_fields (core.lib.models.ScoreVariant attribute)

P

parse_genome_build() (core.lib.models.CatalogScoreHeader class method) (core.lib.models.ScoreHeader class method) parse_weight_type() (core.lib.models.CatalogScoreHeader class method) path (calc.lib.legacy.polygenicscore.AggregatedPGS property) (calc.lib.legacy.polygenicscore.PolygenicScore property) (match.lib.targetvariants.TargetVariants property) Pathish (in module calc.lib.types) PathishList (in module calc.lib.types) paths (calc.lib.scorefile.Scorefiles property) pca (calc.lib.legacy.polygenicscore.AdjustResults attribute) pgp_id (core.lib.models.CatalogScoreHeader attribute) pgs (calc.lib.legacy.polygenicscore.AdjustResults attribute) pgs_id (core.lib.catalogapi.ScoreQueryResult attribute) (core.lib.models.ScoreHeader attribute) (core.lib.models.ScoreLog property) (core.lib.scorefiles.ScoringFile property)

pgs_name (core.lib.models.ScoreHeader attribute) PlinkScoreFiles (class in match.lib.plinkscorefiles) PolygenicScore (class in calc.lib.legacy.polygenicscore) pop_type (calc.lib.legacy.principalcomponents.PrincipalComponents property) poplabel (calc.lib.legacy.principalcomponents.PrincipalComponents property) PopulationType (class in calc.lib.legacy.principalcomponents) pos (match.lib.targetvariants.TargetVariant attribute) PrincipalComponents (class in calc.lib.legacy.principalcomponents) psam_path (calc.lib.legacy.principalcomponents.PrincipalComponents property) pThreshold (calc.lib.legacy.polygenicscore.AdjustArguments attribute) PUBLICATION (core.lib.catalogapi.CatalogCategory attribute) PVAR (match.lib.targetvariants.TargetType attribute)

Q

QueryError

R

read() (calc.lib.legacy.polygenicscore.PolygenicScore method) (core.lib.scorefiles.ScoringFile method) read_bim() (in module match.lib.targetvariants) read_pvar() (in module match.lib.targetvariants) read_variants() (core.lib.scorefiles.ScoringFile method) RECESSIVE (core.lib.effecttype.EffectType attribute) ref (calc.lib.cache.zarrmodels.ZarrVariantMetadata attribute) (match.lib.targetvariants.TargetVariant attribute)

REFERENCE (calc.lib.legacy.principalcomponents.PopulationType attribute) related_path (calc.lib.legacy.principalcomponents.PrincipalComponents property) root (calc.lib.cache.zarrmodels.ZarrSampleMetadata attribute) (core.lib.models.ScoreLogs attribute) row_count (core.lib.models.ScoreHeader property) row_nr (core.lib.models.ScoreVariant attribute) rsID (core.lib.models.CatalogScoreVariant attribute)

S

samples (calc.lib.cache.targetgenome.TargetGenome property) (calc.lib.cache.targetvariants.TargetVariants property) sampleset (calc.lib.cache.targetgenome.TargetGenome property) (calc.lib.score.scorepipeline.ScorePipeline property) samplesets (calc.lib.score.scorepipeline.ScorePipeline property) SamplesheetError SamplesheetFormatError save_ipc() (match.lib.scoringfileframe.ScoringFileFrame method) (match.lib.variantframe.VariantFrame method) SCORE (core.lib.catalogapi.CatalogCategory attribute) score_query() (core.lib.catalogapi.CatalogQuery method) ScoreChecksumError scorecols (calc.lib.legacy.polygenicscore.AdjustResults attribute) ScoreDownloadError Scorefiles (class in calc.lib.scorefile) ScoreFormatError

ScoreFormatVersion (class in core.lib.models) ScoreHeader (class in core.lib.models) ScoreLog (class in core.lib.models) ScoreLogs (class in core.lib.models) ScorePipeline (class in calc.lib.score.scorepipeline) ScoreQueryResult (class in core.lib.catalogapi) ScoreVariant (class in core.lib.models) ScoringFile (class in core.lib.scorefiles) ScoringFileFrame (class in match.lib.scoringfileframe) ScoringFiles (class in core.lib.scorefiles) serialize() (core.lib.models.Allele method) serialize_genomebuild() (core.lib.models.CatalogScoreHeader method) (core.lib.models.ScoreHeader method) set_missing_rsid() (core.lib.models.CatalogScoreVariant class method) sources (core.lib.models.ScoreLog property) split_traits() (core.lib.models.CatalogScoreHeader class method) summary_log (match.lib.matchresult.MatchResults property)

T

TARGET (calc.lib.legacy.principalcomponents.PopulationType attribute) target_build (core.lib.scorefiles.ScoringFile property) (core.lib.scorefiles.ScoringFiles attribute) target_label (calc.lib.legacy.polygenicscore.AdjustResults attribute) target_name (calc.lib.legacy.polygenicscore.AggregatedPGS property) target_path (calc.lib.cache.targetgenome.TargetGenome property) target_variants_columns (calc.lib.score.scorepipeline.ScorePipeline property) TargetGenome (class in calc.lib.cache.targetgenome) TargetType (class in match.lib.targetvariants)

TargetVariant (class in match.lib.targetvariants) TargetVariants (class in calc.lib.cache.targetvariants) (class in match.lib.targetvariants) to_df() (calc.lib.cache.zarrmodels.ZarrVariantMetadata method) to_numpy() (calc.lib.cache.zarrmodels.ZarrVariantMetadata method) TRAIT (core.lib.catalogapi.CatalogCategory attribute) trait_efo (core.lib.models.CatalogScoreHeader attribute) trait_mapped (core.lib.models.CatalogScoreHeader attribute) trait_reported (core.lib.models.ScoreHeader attribute)

V

v2 (core.lib.models.ScoreFormatVersion attribute) VALID_CHROMOSOMES (in module calc.lib.constants) variant_count_difference (core.lib.models.ScoreLog property) variant_description (core.lib.models.CatalogScoreVariant attribute) variant_id (calc.lib.cache.zarrmodels.ZarrVariantMetadata attribute) (core.lib.models.CatalogScoreVariant property) variant_ids (calc.lib.cache.targetvariants.TargetVariants property) variant_logs (core.lib.models.ScoreLog attribute) variant_metadata (calc.lib.cache.targetvariants.TargetVariants property) variant_type (core.lib.models.CatalogScoreVariant attribute)

VariantFrame (class in match.lib.variantframe) VariantLog (class in core.lib.models) variants (core.lib.scorefiles.ScoringFile property) (match.lib.normalisedscoringfile.NormalisedScoringFile property) (match.lib.targetvariants.TargetVariants property) (match.lib.variantframe.VariantFrame attribute) variants_are_missing (core.lib.models.ScoreLog property) variants_number (core.lib.models.CatalogScoreHeader attribute) VariantType (class in core.lib.models) VCF (calc.lib.cache.genomefiletypes.GenomeFileType attribute)

W

weight_type (core.lib.models.CatalogScoreHeader attribute) write() (calc.lib.legacy.polygenicscore.AdjustResults method) (calc.lib.legacy.polygenicscore.PolygenicScore method)

write_scorefiles() (match.lib.matchresult.MatchResults method) write_zarr() (calc.lib.cache.targetvariants.TargetVariants method)

Z

ZARR_COMPRESSOR (calc.lib.config.Config attribute) zarr_group (calc.lib.cache.targetgenome.TargetGenome property) ZARR_PLOIDY (in module calc.lib.constants)

ZARR_VARIANT_CHUNK_SIZE (calc.lib.config.Config attribute) ZarrSampleMetadata (class in calc.lib.cache.zarrmodels) ZarrVariantMetadata (class in calc.lib.cache.zarrmodels) ZeroMatchesError