Index
A
|
B
|
C
|
D
|
E
|
F
|
G
|
H
|
I
|
L
|
M
|
N
|
O
|
P
|
Q
|
R
|
S
|
T
|
V
|
W
|
Z
A
ADDITIVE (pgscatalog.core.EffectType attribute)
(pgscatalog.core.lib.EffectType attribute)
(pgscatalog.core.lib.scorevariant.EffectType attribute)
adjust() (pgscatalog.calc.AggregatedPGS method)
(pgscatalog.calc.lib.AggregatedPGS method)
(pgscatalog.calc.lib.polygenicscore.AggregatedPGS method)
AdjustArguments (class in pgscatalog.calc)
(class in pgscatalog.calc.lib)
(class in pgscatalog.calc.lib.polygenicscore)
AdjustResults (class in pgscatalog.calc)
(class in pgscatalog.calc.lib)
(class in pgscatalog.calc.lib.polygenicscore)
AggregatedPGS (class in pgscatalog.calc)
(class in pgscatalog.calc.lib)
(class in pgscatalog.calc.lib.polygenicscore)
allele (pgscatalog.core.lib.scorevariant.EffectAllele property)
annotate_multiallelic() (in module pgscatalog.match.lib._match.preprocess)
API_HEADER (pgscatalog.core.Config attribute)
(pgscatalog.core.lib._config.Config attribute)
(pgscatalog.core.lib.Config attribute)
assign_effect_type() (in module pgscatalog.core.lib._normalise)
assign_other_allele() (in module pgscatalog.core.lib._normalise)
average() (pgscatalog.calc.lib.PolygenicScore method)
(pgscatalog.calc.lib.polygenicscore.PolygenicScore method)
(pgscatalog.calc.PolygenicScore method)
B
BasePGSException
,
[1]
,
[2]
BATCH_SIZE (pgscatalog.core.Config attribute)
(pgscatalog.core.lib._config.Config attribute)
(pgscatalog.core.lib.Config attribute)
BIM (pgscatalog.core.lib.targetvariants.TargetType attribute)
BuildError
,
[1]
,
[2]
C
CatalogCategory (class in pgscatalog.core)
(class in pgscatalog.core.lib)
(class in pgscatalog.core.lib.catalogapi)
CatalogError
,
[1]
,
[2]
CatalogQuery (class in pgscatalog.core)
(class in pgscatalog.core.lib)
(class in pgscatalog.core.lib.catalogapi)
check_bad_variant() (in module pgscatalog.core.lib._normalise)
check_duplicates() (in module pgscatalog.core.lib._normalise)
check_effect_allele() (in module pgscatalog.core.lib._normalise)
check_effect_weight() (in module pgscatalog.core.lib._normalise)
check_log_count() (in module pgscatalog.match.lib._match.log)
choose_pval_threshold() (in module pgscatalog.calc.lib._ancestry.tools)
chrom (pgscatalog.core.lib.TargetVariants property)
(pgscatalog.core.lib.targetvariants.TargetVariants property)
(pgscatalog.core.TargetVariants property)
code_map (pgscatalog.core.lib.pgsexceptions.ExceptionExitCodeMap attribute)
collect() (pgscatalog.match.lib.MatchResult method)
(pgscatalog.match.lib.matchresult.MatchResult method)
(pgscatalog.match.MatchResult method)
CombineError
,
[1]
,
[2]
compare_ancestry() (in module pgscatalog.calc.lib._ancestry.tools)
comparison_method_threshold (in module pgscatalog.calc.lib._ancestry.tools)
complement_valid_alleles() (in module pgscatalog.match.lib._match.preprocess)
complex_fields (pgscatalog.core.lib.ScoreVariant attribute)
(pgscatalog.core.lib.scorevariant.ScoreVariant attribute)
(pgscatalog.core.ScoreVariant attribute)
Config (class in pgscatalog.calc.lib._config)
(class in pgscatalog.core)
(class in pgscatalog.core.lib)
(class in pgscatalog.core.lib._config)
(class in pgscatalog.match.lib._config)
D
default() (pgscatalog.calc.lib._ancestry.tools.NumpyEncoder method)
detect_complex() (in module pgscatalog.core.lib._normalise)
detect_wide() (in module pgscatalog.core.lib._read)
df (pgscatalog.calc.AggregatedPGS property)
(pgscatalog.calc.lib.AggregatedPGS property)
(pgscatalog.calc.lib.PolygenicScore property)
(pgscatalog.calc.lib.polygenicscore.AggregatedPGS property)
(pgscatalog.calc.lib.polygenicscore.PolygenicScore property)
(pgscatalog.calc.lib.PrincipalComponents property)
(pgscatalog.calc.lib.principalcomponents.PrincipalComponents property)
(pgscatalog.calc.PolygenicScore property)
(pgscatalog.calc.PrincipalComponents property)
DOMINANT (pgscatalog.core.EffectType attribute)
(pgscatalog.core.lib.EffectType attribute)
(pgscatalog.core.lib.scorevariant.EffectType attribute)
download() (pgscatalog.core.lib.scorefiles.ScoringFile method)
(pgscatalog.core.lib.ScoringFile method)
(pgscatalog.core.ScoringFile method)
drop_hla() (in module pgscatalog.core.lib._normalise)
DuplicateMatchError
,
[1]
,
[2]
E
EffectAllele (class in pgscatalog.core.lib.scorevariant)
EffectType (class in pgscatalog.core)
(class in pgscatalog.core.lib)
(class in pgscatalog.core.lib.scorevariant)
elements (pgscatalog.core.lib.scorefiles.ScoringFiles property)
(pgscatalog.core.lib.ScoringFiles property)
(pgscatalog.core.ScoringFiles property)
ExceptionExitCodeMap (class in pgscatalog.core.lib.pgsexceptions)
extract_ref_psam_cols() (in module pgscatalog.calc.lib._ancestry.read)
F
f_mu() (in module pgscatalog.calc.lib._ancestry.tools)
f_var() (in module pgscatalog.calc.lib._ancestry.tools)
fields (pgscatalog.core.lib.scorefiles.ScoringFileHeader attribute)
filter() (pgscatalog.match.lib.matchresult.MatchResults method)
(pgscatalog.match.lib.MatchResults method)
(pgscatalog.match.MatchResults method)
filter_scores() (in module pgscatalog.match.lib._match.filter)
filter_target() (in module pgscatalog.match.lib._match.preprocess)
from_ipc() (pgscatalog.match.lib.MatchResult class method)
(pgscatalog.match.lib.matchresult.MatchResult class method)
(pgscatalog.match.MatchResult class method)
from_matchresult() (pgscatalog.match.lib._plinkframe.PlinkFrames class method)
from_path() (pgscatalog.core.lib.scorefiles.ScoringFileHeader class method)
from_query() (pgscatalog.core.lib.catalogapi.ScoreQueryResult class method)
(pgscatalog.core.lib.ScoreQueryResult class method)
(pgscatalog.core.ScoreQueryResult class method)
from_string() (pgscatalog.core.GenomeBuild class method)
(pgscatalog.core.lib.GenomeBuild class method)
(pgscatalog.core.lib.genomebuild.GenomeBuild class method)
FTP_EXCLUSIVE (pgscatalog.core.Config attribute)
(pgscatalog.core.lib._config.Config attribute)
(pgscatalog.core.lib.Config attribute)
ftp_fallback() (in module pgscatalog.core.lib._download)
full_variant_log() (pgscatalog.match.lib.matchresult.MatchResults method)
(pgscatalog.match.lib.MatchResults method)
(pgscatalog.match.MatchResults method)
fullLL_adjust() (in module pgscatalog.calc.lib._ancestry.tools)
fullLL_fit() (in module pgscatalog.calc.lib._ancestry.tools)
G
generate_header_lines() (in module pgscatalog.core.lib._read)
GenomeBuild (class in pgscatalog.core)
(class in pgscatalog.core.lib)
(class in pgscatalog.core.lib.genomebuild)
GenomesNotFound
,
[1]
,
[2]
get_all_matches() (in module pgscatalog.match.lib._match.match)
get_columns() (in module pgscatalog.core.lib._read)
get_covariance_method() (in module pgscatalog.calc.lib._ancestry.tools)
get_download_url() (pgscatalog.core.lib.catalogapi.ScoreQueryResult method)
(pgscatalog.core.lib.ScoreQueryResult method)
(pgscatalog.core.ScoreQueryResult method)
get_log() (pgscatalog.core.lib.scorefiles.ScoringFile method)
(pgscatalog.core.lib.ScoringFile method)
(pgscatalog.core.ScoringFile method)
get_query_url() (pgscatalog.core.CatalogQuery method)
(pgscatalog.core.lib.catalogapi.CatalogQuery method)
(pgscatalog.core.lib.CatalogQuery method)
GRCh37 (pgscatalog.core.GenomeBuild attribute)
(pgscatalog.core.lib.GenomeBuild attribute)
(pgscatalog.core.lib.genomebuild.GenomeBuild attribute)
GRCh38 (pgscatalog.core.GenomeBuild attribute)
(pgscatalog.core.lib.GenomeBuild attribute)
(pgscatalog.core.lib.genomebuild.GenomeBuild attribute)
grdnt_mu_and_var() (in module pgscatalog.calc.lib._ancestry.tools)
H
handle_uncaught_exception() (in module pgscatalog.core.lib.pgsexceptions)
https_download() (in module pgscatalog.core.lib._download)
I
infer_category() (pgscatalog.core.CatalogQuery method)
(pgscatalog.core.lib.catalogapi.CatalogQuery method)
(pgscatalog.core.lib.CatalogQuery method)
InvalidAccessionError
,
[1]
,
[2]
is_snp (pgscatalog.core.lib.scorevariant.EffectAllele property)
L
label() (pgscatalog.match.lib.matchresult.MatchResults method)
(pgscatalog.match.lib.MatchResults method)
(pgscatalog.match.MatchResults method)
label_matches() (in module pgscatalog.match.lib._match.label)
lazy_read() (pgscatalog.calc.lib.PolygenicScore method)
(pgscatalog.calc.lib.polygenicscore.PolygenicScore method)
(pgscatalog.calc.PolygenicScore method)
lift() (in module pgscatalog.core.lib._normalise)
LiftoverError
load_chain() (in module pgscatalog.core.lib._normalise)
logger (in module pgscatalog.calc.lib._ancestry.read)
(in module pgscatalog.calc.lib._ancestry.tools)
(in module pgscatalog.calc.lib.polygenicscore)
(in module pgscatalog.calc.lib.principalcomponents)
(in module pgscatalog.core.lib._download)
(in module pgscatalog.core.lib._normalise)
(in module pgscatalog.core.lib._read)
(in module pgscatalog.core.lib._relabel)
(in module pgscatalog.core.lib.catalogapi)
(in module pgscatalog.core.lib.scorefiles)
(in module pgscatalog.match.lib._match.filter)
(in module pgscatalog.match.lib._match.label)
(in module pgscatalog.match.lib._match.log)
(in module pgscatalog.match.lib._match.match)
(in module pgscatalog.match.lib._match.plink)
(in module pgscatalog.match.lib._match.preprocess)
(in module pgscatalog.match.lib.matchresult)
(in module pgscatalog.match.lib.scoringfileframe)
(in module pgscatalog.match.lib.variantframe)
loose() (in module pgscatalog.match.lib._arrow)
M
make_logs() (in module pgscatalog.match.lib._match.log)
make_summary_log() (in module pgscatalog.match.lib._match.log)
mandatory_fields (pgscatalog.core.lib.ScoreVariant attribute)
(pgscatalog.core.lib.scorevariant.ScoreVariant attribute)
(pgscatalog.core.ScoreVariant attribute)
match_variants() (in module pgscatalog.match)
(in module pgscatalog.match.lib)
(in module pgscatalog.match.lib._match.match)
(in module pgscatalog.match.lib.scoringfileframe)
MatchError
,
[1]
,
[2]
MatchRateError
,
[1]
,
[2]
MatchResult (class in pgscatalog.match)
(class in pgscatalog.match.lib)
(class in pgscatalog.match.lib.matchresult)
MatchResults (class in pgscatalog.match)
(class in pgscatalog.match.lib)
(class in pgscatalog.match.lib.matchresult)
MatchValueError
,
[1]
,
[2]
max_pcs (pgscatalog.calc.lib.PrincipalComponents property)
(pgscatalog.calc.lib.principalcomponents.PrincipalComponents property)
(pgscatalog.calc.PrincipalComponents property)
MAX_RETRIES (pgscatalog.core.Config attribute)
(pgscatalog.core.lib._config.Config attribute)
(pgscatalog.core.lib.Config attribute)
melt() (pgscatalog.calc.lib.PolygenicScore method)
(pgscatalog.calc.lib.polygenicscore.PolygenicScore method)
(pgscatalog.calc.PolygenicScore method)
merge() (pgscatalog.match.lib.PlinkScoreFiles method)
(pgscatalog.match.lib.plinkscorefiles.PlinkScoreFiles method)
(pgscatalog.match.PlinkScoreFiles method)
method_compare (pgscatalog.calc.AdjustArguments attribute)
(pgscatalog.calc.lib.AdjustArguments attribute)
(pgscatalog.calc.lib.polygenicscore.AdjustArguments attribute)
method_normalization (pgscatalog.calc.AdjustArguments attribute)
(pgscatalog.calc.lib.AdjustArguments attribute)
(pgscatalog.calc.lib.polygenicscore.AdjustArguments attribute)
model_meta (pgscatalog.calc.AdjustResults attribute)
(pgscatalog.calc.lib.AdjustResults attribute)
(pgscatalog.calc.lib.polygenicscore.AdjustResults attribute)
models (pgscatalog.calc.AdjustResults attribute)
(pgscatalog.calc.lib.AdjustResults attribute)
(pgscatalog.calc.lib.polygenicscore.AdjustResults attribute)
module
pgscatalog.calc
pgscatalog.calc.cli
pgscatalog.calc.cli.aggregate_cli
pgscatalog.calc.cli.ancestry_cli
pgscatalog.calc.lib
pgscatalog.calc.lib._ancestry
pgscatalog.calc.lib._ancestry.read
pgscatalog.calc.lib._ancestry.tools
pgscatalog.calc.lib._config
pgscatalog.calc.lib.polygenicscore
pgscatalog.calc.lib.principalcomponents
pgscatalog.core
pgscatalog.core.cli
pgscatalog.core.cli._combine
pgscatalog.core.cli.combine_cli
pgscatalog.core.cli.download_cli
pgscatalog.core.cli.relabel_cli
pgscatalog.core.lib
pgscatalog.core.lib._config
pgscatalog.core.lib._download
pgscatalog.core.lib._normalise
pgscatalog.core.lib._read
pgscatalog.core.lib._relabel
pgscatalog.core.lib.catalogapi
pgscatalog.core.lib.genomebuild
pgscatalog.core.lib.pgsexceptions
pgscatalog.core.lib.scorefiles
pgscatalog.core.lib.scorevariant
pgscatalog.core.lib.targetvariants
pgscatalog.match
pgscatalog.match.cli
pgscatalog.match.cli._config
pgscatalog.match.cli._write
pgscatalog.match.cli.match_cli
pgscatalog.match.cli.merge_cli
pgscatalog.match.lib
pgscatalog.match.lib._arrow
pgscatalog.match.lib._config
pgscatalog.match.lib._match
pgscatalog.match.lib._match.filter
pgscatalog.match.lib._match.label
pgscatalog.match.lib._match.log
pgscatalog.match.lib._match.match
pgscatalog.match.lib._match.plink
pgscatalog.match.lib._match.preprocess
pgscatalog.match.lib._plinkframe
pgscatalog.match.lib.matchresult
pgscatalog.match.lib.plinkscorefiles
pgscatalog.match.lib.scoringfileframe
pgscatalog.match.lib.variantframe
N
NCBI35 (pgscatalog.core.GenomeBuild attribute)
(pgscatalog.core.lib.GenomeBuild attribute)
(pgscatalog.core.lib.genomebuild.GenomeBuild attribute)
NCBI36 (pgscatalog.core.GenomeBuild attribute)
(pgscatalog.core.lib.GenomeBuild attribute)
(pgscatalog.core.lib.genomebuild.GenomeBuild attribute)
nLL_mu_and_var() (in module pgscatalog.calc.lib._ancestry.tools)
normalise() (in module pgscatalog.core.lib._normalise)
(pgscatalog.core.lib.scorefiles.ScoringFile method)
(pgscatalog.core.lib.ScoringFile method)
(pgscatalog.core.ScoringFile method)
NormalisedScoringFile (class in pgscatalog.core)
(class in pgscatalog.core.lib)
(class in pgscatalog.core.lib.scorefiles)
normalization_methods (in module pgscatalog.calc.lib._ancestry.tools)
npcs_norm (pgscatalog.calc.lib.PrincipalComponents property)
(pgscatalog.calc.lib.principalcomponents.PrincipalComponents property)
(pgscatalog.calc.PrincipalComponents property)
npcs_popcomp (pgscatalog.calc.lib.PrincipalComponents property)
(pgscatalog.calc.lib.principalcomponents.PrincipalComponents property)
(pgscatalog.calc.PrincipalComponents property)
NumpyEncoder (class in pgscatalog.calc.lib._ancestry.tools)
O
optional_fields (pgscatalog.core.lib.ScoreVariant attribute)
(pgscatalog.core.lib.scorevariant.ScoreVariant attribute)
(pgscatalog.core.ScoreVariant attribute)
output_fields (pgscatalog.core.lib.ScoreVariant attribute)
(pgscatalog.core.lib.scorevariant.ScoreVariant attribute)
(pgscatalog.core.ScoreVariant attribute)
P
pa_schema() (pgscatalog.core.lib.NormalisedScoringFile method)
(pgscatalog.core.lib.scorefiles.NormalisedScoringFile method)
(pgscatalog.core.lib.TargetVariants method)
(pgscatalog.core.lib.targetvariants.TargetVariants method)
(pgscatalog.core.NormalisedScoringFile method)
(pgscatalog.core.TargetVariants method)
package_skl_regression() (in module pgscatalog.calc.lib._ancestry.tools)
path (pgscatalog.calc.AggregatedPGS property)
(pgscatalog.calc.lib.AggregatedPGS property)
(pgscatalog.calc.lib.polygenicscore.AggregatedPGS property)
(pgscatalog.core.lib.TargetVariants property)
(pgscatalog.core.lib.targetvariants.TargetVariants property)
(pgscatalog.core.TargetVariants property)
pca (pgscatalog.calc.AdjustResults attribute)
(pgscatalog.calc.lib.AdjustResults attribute)
(pgscatalog.calc.lib.polygenicscore.AdjustResults attribute)
pgs (pgscatalog.calc.AdjustResults attribute)
(pgscatalog.calc.lib.AdjustResults attribute)
(pgscatalog.calc.lib.polygenicscore.AdjustResults attribute)
pgs_adjust() (in module pgscatalog.calc.lib._ancestry.tools)
pgscatalog.calc
module
pgscatalog.calc.cli
module
pgscatalog.calc.cli.aggregate_cli
module
pgscatalog.calc.cli.ancestry_cli
module
pgscatalog.calc.lib
module
pgscatalog.calc.lib._ancestry
module
pgscatalog.calc.lib._ancestry.read
module
pgscatalog.calc.lib._ancestry.tools
module
pgscatalog.calc.lib._config
module
pgscatalog.calc.lib.polygenicscore
module
pgscatalog.calc.lib.principalcomponents
module
pgscatalog.core
module
pgscatalog.core.cli
module
pgscatalog.core.cli._combine
module
pgscatalog.core.cli.combine_cli
module
pgscatalog.core.cli.download_cli
module
pgscatalog.core.cli.relabel_cli
module
pgscatalog.core.lib
module
pgscatalog.core.lib._config
module
pgscatalog.core.lib._download
module
pgscatalog.core.lib._normalise
module
pgscatalog.core.lib._read
module
pgscatalog.core.lib._relabel
module
pgscatalog.core.lib.catalogapi
module
pgscatalog.core.lib.genomebuild
module
pgscatalog.core.lib.pgsexceptions
module
pgscatalog.core.lib.scorefiles
module
pgscatalog.core.lib.scorevariant
module
pgscatalog.core.lib.targetvariants
module
pgscatalog.match
module
pgscatalog.match.cli
module
pgscatalog.match.cli._config
module
pgscatalog.match.cli._write
module
pgscatalog.match.cli.match_cli
module
pgscatalog.match.cli.merge_cli
module
pgscatalog.match.lib
module
pgscatalog.match.lib._arrow
module
pgscatalog.match.lib._config
module
pgscatalog.match.lib._match
module
pgscatalog.match.lib._match.filter
module
pgscatalog.match.lib._match.label
module
pgscatalog.match.lib._match.log
module
pgscatalog.match.lib._match.match
module
pgscatalog.match.lib._match.plink
module
pgscatalog.match.lib._match.preprocess
module
pgscatalog.match.lib._plinkframe
module
pgscatalog.match.lib.matchresult
module
pgscatalog.match.lib.plinkscorefiles
module
pgscatalog.match.lib.scoringfileframe
module
pgscatalog.match.lib.variantframe
module
pivot_score() (in module pgscatalog.match.lib._match.plink)
pivot_wide() (pgscatalog.match.lib._plinkframe.PlinkFrame method)
PlinkFrame (class in pgscatalog.match.lib._plinkframe)
PlinkFrames (class in pgscatalog.match.lib._plinkframe)
plinkify() (in module pgscatalog.match.lib._match.plink)
PlinkScoreFiles (class in pgscatalog.match)
(class in pgscatalog.match.lib)
(class in pgscatalog.match.lib.plinkscorefiles)
PolygenicScore (class in pgscatalog.calc)
(class in pgscatalog.calc.lib)
(class in pgscatalog.calc.lib.polygenicscore)
pop_type (pgscatalog.calc.lib.PrincipalComponents property)
(pgscatalog.calc.lib.principalcomponents.PrincipalComponents property)
(pgscatalog.calc.PrincipalComponents property)
poplabel (pgscatalog.calc.lib.PrincipalComponents property)
(pgscatalog.calc.lib.principalcomponents.PrincipalComponents property)
(pgscatalog.calc.PrincipalComponents property)
PopulationType (class in pgscatalog.calc)
(class in pgscatalog.calc.lib)
(class in pgscatalog.calc.lib.principalcomponents)
PrincipalComponents (class in pgscatalog.calc)
(class in pgscatalog.calc.lib)
(class in pgscatalog.calc.lib.principalcomponents)
psam_path (pgscatalog.calc.lib.PrincipalComponents property)
(pgscatalog.calc.lib.principalcomponents.PrincipalComponents property)
(pgscatalog.calc.PrincipalComponents property)
pThreshold (pgscatalog.calc.AdjustArguments attribute)
(pgscatalog.calc.lib.AdjustArguments attribute)
(pgscatalog.calc.lib.polygenicscore.AdjustArguments attribute)
PUBLICATION (pgscatalog.core.CatalogCategory attribute)
(pgscatalog.core.lib.catalogapi.CatalogCategory attribute)
(pgscatalog.core.lib.CatalogCategory attribute)
PVAR (pgscatalog.core.lib.targetvariants.TargetType attribute)
PYARROW_AVAILABLE (in module pgscatalog.core.lib.scorefiles)
(in module pgscatalog.core.lib.targetvariants)
Q
QueryError
,
[1]
,
[2]
R
read() (pgscatalog.calc.lib.PolygenicScore method)
(pgscatalog.calc.lib.polygenicscore.PolygenicScore method)
(pgscatalog.calc.PolygenicScore method)
read_bim() (in module pgscatalog.core.lib.targetvariants)
read_header() (in module pgscatalog.core.lib._read)
read_pcs() (in module pgscatalog.calc.lib._ancestry.read)
read_pgs() (in module pgscatalog.calc.lib._ancestry.read)
read_pvar() (in module pgscatalog.core.lib.targetvariants)
read_rows_lazy() (in module pgscatalog.core.lib._read)
RECESSIVE (pgscatalog.core.EffectType attribute)
(pgscatalog.core.lib.EffectType attribute)
(pgscatalog.core.lib.scorevariant.EffectType attribute)
REFERENCE (pgscatalog.calc.lib.PopulationType attribute)
(pgscatalog.calc.lib.principalcomponents.PopulationType attribute)
(pgscatalog.calc.PopulationType attribute)
relabel() (in module pgscatalog.core)
(in module pgscatalog.core.lib)
(in module pgscatalog.core.lib._relabel)
relabel_write() (in module pgscatalog.core)
(in module pgscatalog.core.lib)
(in module pgscatalog.core.lib._relabel)
RelabelArgs (in module pgscatalog.core)
(in module pgscatalog.core.lib)
(in module pgscatalog.core.lib._relabel)
related_path (pgscatalog.calc.lib.PrincipalComponents property)
(pgscatalog.calc.lib.principalcomponents.PrincipalComponents property)
(pgscatalog.calc.PrincipalComponents property)
remap_harmonised() (in module pgscatalog.core.lib._normalise)
ROOT_DIR (pgscatalog.calc.lib._config.Config attribute)
(pgscatalog.core.Config attribute)
(pgscatalog.core.lib._config.Config attribute)
(pgscatalog.core.lib.Config attribute)
(pgscatalog.match.lib._config.Config attribute)
S
SamplesheetError
,
[1]
,
[2]
SamplesheetFormatError
,
[1]
,
[2]
save_ipc() (pgscatalog.match.lib.ScoringFileFrame method)
(pgscatalog.match.lib.scoringfileframe.ScoringFileFrame method)
(pgscatalog.match.lib.VariantFrame method)
(pgscatalog.match.lib.variantframe.VariantFrame method)
(pgscatalog.match.ScoringFileFrame method)
(pgscatalog.match.VariantFrame method)
SCORE (pgscatalog.core.CatalogCategory attribute)
(pgscatalog.core.lib.catalogapi.CatalogCategory attribute)
(pgscatalog.core.lib.CatalogCategory attribute)
score_download_failed() (in module pgscatalog.core.lib._download)
score_query() (pgscatalog.core.CatalogQuery method)
(pgscatalog.core.lib.catalogapi.CatalogQuery method)
(pgscatalog.core.lib.CatalogQuery method)
ScoreChecksumError
,
[1]
,
[2]
scorecols (pgscatalog.calc.AdjustResults attribute)
(pgscatalog.calc.lib.AdjustResults attribute)
(pgscatalog.calc.lib.polygenicscore.AdjustResults attribute)
ScoreDownloadError
,
[1]
,
[2]
ScoreFormatError
,
[1]
,
[2]
ScoreQueryResult (class in pgscatalog.core)
(class in pgscatalog.core.lib)
(class in pgscatalog.core.lib.catalogapi)
ScoreVariant (class in pgscatalog.core)
(class in pgscatalog.core.lib)
(class in pgscatalog.core.lib.scorevariant)
ScoringFile (class in pgscatalog.core)
(class in pgscatalog.core.lib)
(class in pgscatalog.core.lib.scorefiles)
ScoringFileFrame (class in pgscatalog.match)
(class in pgscatalog.match.lib)
(class in pgscatalog.match.lib.scoringfileframe)
ScoringFileHeader (class in pgscatalog.core.lib.scorefiles)
ScoringFiles (class in pgscatalog.core)
(class in pgscatalog.core.lib)
(class in pgscatalog.core.lib.scorefiles)
split_pivot() (pgscatalog.match.lib._plinkframe.PlinkFrame method)
T
TARGET (pgscatalog.calc.lib.PopulationType attribute)
(pgscatalog.calc.lib.principalcomponents.PopulationType attribute)
(pgscatalog.calc.PopulationType attribute)
TARGET_BATCH_SIZE (pgscatalog.core.Config attribute)
(pgscatalog.core.lib._config.Config attribute)
(pgscatalog.core.lib.Config attribute)
target_build (pgscatalog.core.lib.scorefiles.ScoringFile property)
(pgscatalog.core.lib.ScoringFile property)
(pgscatalog.core.ScoringFile property)
target_label (pgscatalog.calc.AdjustResults attribute)
(pgscatalog.calc.lib.AdjustResults attribute)
(pgscatalog.calc.lib.polygenicscore.AdjustResults attribute)
target_name (pgscatalog.calc.AggregatedPGS property)
(pgscatalog.calc.lib.AggregatedPGS property)
(pgscatalog.calc.lib.polygenicscore.AggregatedPGS property)
TargetType (class in pgscatalog.core.lib.targetvariants)
TargetVariant (class in pgscatalog.core)
(class in pgscatalog.core.lib)
(class in pgscatalog.core.lib.targetvariants)
TargetVariants (class in pgscatalog.core)
(class in pgscatalog.core.lib)
(class in pgscatalog.core.lib.targetvariants)
to_pa_recordbatch() (pgscatalog.core.lib.NormalisedScoringFile method)
(pgscatalog.core.lib.scorefiles.NormalisedScoringFile method)
(pgscatalog.core.lib.TargetVariants method)
(pgscatalog.core.lib.targetvariants.TargetVariants method)
(pgscatalog.core.NormalisedScoringFile method)
(pgscatalog.core.TargetVariants method)
TRAIT (pgscatalog.core.CatalogCategory attribute)
(pgscatalog.core.lib.catalogapi.CatalogCategory attribute)
(pgscatalog.core.lib.CatalogCategory attribute)
V
VariantFrame (class in pgscatalog.match)
(class in pgscatalog.match.lib)
(class in pgscatalog.match.lib.variantframe)
variants (pgscatalog.core.lib.NormalisedScoringFile property)
(pgscatalog.core.lib.scorefiles.NormalisedScoringFile property)
(pgscatalog.core.lib.scorefiles.ScoringFile property)
(pgscatalog.core.lib.ScoringFile property)
(pgscatalog.core.lib.TargetVariants property)
(pgscatalog.core.lib.targetvariants.TargetVariants property)
(pgscatalog.core.NormalisedScoringFile property)
(pgscatalog.core.ScoringFile property)
(pgscatalog.core.TargetVariants property)
W
write() (pgscatalog.calc.AdjustResults method)
(pgscatalog.calc.lib.AdjustResults method)
(pgscatalog.calc.lib.PolygenicScore method)
(pgscatalog.calc.lib.polygenicscore.AdjustResults method)
(pgscatalog.calc.lib.polygenicscore.PolygenicScore method)
(pgscatalog.calc.PolygenicScore method)
(pgscatalog.match.lib._plinkframe.PlinkFrame method)
write_model() (in module pgscatalog.calc.lib._ancestry.tools)
write_scorefiles() (pgscatalog.match.lib.matchresult.MatchResults method)
(pgscatalog.match.lib.MatchResults method)
(pgscatalog.match.MatchResults method)
Z
ZeroMatchesError
,
[1]
,
[2]
pygscatalog
Navigation
Links
GitHub
Contents:
How-to guides
API Reference
Related Topics
Documentation overview
Quick search