scores-class {quincunx}

An S4 class to represent a set of PGS Catalog Polygenic Scores

Description

The scores object consists of six tables (slots) that combined form a relational database of a subset of PGS Catalog polygenic scores. Each score is an observation (row) in the scores table (the first table).

Slots

scores

A table of polygenic scores. Each polygenic score (row) is uniquely identified by the pgs_id column. Columns:

pgs_id

Polygenic Score (PGS) identifier. Example: "PGS000001".

pgs_name

This may be the name that the authors describe the PGS with in the source publication, or a name that a curator of the PGS Catalog has assigned to identify the score during the curation process (before a PGS identifier has been given). Example: PRS77_BC.

scoring_file

URL to the scoring file on the PGS FTP server. Example: "http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000001/ScoringFiles/PGS000001.txt.gz".

matches_publication

Indicate if the PGS data matches the published polygenic score (TRUE). If not (FALSE), the authors have provided an alternative polygenic for the Catalog and some other data, such as performance metrics, may differ from the publication.

reported_trait

The author-reported trait that the PGS has been developed to predict. Example: "Breast Cancer".

trait_additional_description

Any additional description not captured in the other columns. Example: "Femoral neck BMD (g/cm2)".

pgs_method_name

The name or description of the method or computational algorithm used to develop the PGS.

pgs_method_params

A description of the relevant inputs and parameters relevant to the PGS development method/process.

n_variants

Number of variants used to calculate the PGS.

n_variants_interactions

Number of higher-order variant interactions included in the PGS.

assembly

The version of the genome assembly that the variants present in the PGS are associated with. Example: GRCh37.

license

The PGS Catalog distributes its data according to EBI's standard Terms of Use. Some PGS have specific terms, licenses, or restrictions (e.g. non-commercial use) that we highlight in this field, if known.

publications

A table of publications. Each publication (row) is uniquely identified by the pgp_id column. Columns:

pgs_id

Polygenic Score (PGS) identifier.

pgp_id

PGS Publication identifier. Example: "PGP000001".

pubmed_id

PubMed identifier. Example: "25855707".

publication_date

Publication date. Example: "2020-09-28". Note that the class of publication_date is Date.

publication

Abbreviated name of the journal. Example: "Am J Hum Genet".

title

Publication title.

author_fullname

First author of the publication. Example: 'Mavaddat N'.

doi

Digital Object Identifier (DOI). This variable is also curated to allow unpublished work (e.g. preprints) to be added to the catalog. Example: "10.1093/jnci/djv036".

samples

A table of samples. Each sample (row) is uniquely identified by the combination of values from the columns: pgs_id and sample_id. Columns:

pgs_id

Polygenic score identifier. An identifier that starts with 'PGS' and is followed by six digits, e.g. 'PGS000001'.

sample_id

Sample identifier. This is a surrogate key to identify each sample.

stage

Sample stage: either "discovery" or "training".

sample_size

Number of individuals included in the sample.

sample_cases

Number of cases.

sample_controls

Number of controls.

sample_percent_male

Percentage of male participants.

phenotype_description

Detailed phenotype description.

ancestry_category

Author reported ancestry is mapped to the best matching ancestry category from the NHGRI-EBI GWAS Catalog framework (see ancestry_categories) for possible values.

ancestry

A more detailed description of sample ancestry that usually matches the most specific description described by the authors (e.g. French, Chinese).

country

Author reported countries of recruitment (if available).

ancestry_additional_description

Any additional description not captured in the other columns (e.g. founder or genetically isolated populations, or further description of admixed samples).

study_id

Associated GWAS Catalog study accession identifier, e.g., "GCST002735".

pubmed_id

PubMed identifier.

cohorts_additional_description

Any additional description about the samples (e.g. sub-cohort information).

demographics

A table of sample demographics' variables. Each demographics' variable (row) is uniquely identified by the combination of values from the columns: pgs_id, sample_id and variable. Columns:

pgs_id

Polygenic Score (PGS) identifier.

sample_id

Sample identifier. This is a surrogate identifier to identify each sample.

variable

Demographics variable. Following columns report about the indicated variable.

estimate_type

Type of statistical estimate for variable.

estimate

The variable's statistical value.

unit

Unit of the variable.

variability_type

Measure of statistical dispersion for variable, e.g. standard error (se) or standard deviation (sd).

variability

The value of the measure of dispersion.

interval_type

Type of statistical interval for variable: range, iqr (interquartile), ci (confidence interval).

interval_lower

Interval lower bound.

interval_upper

Interval upper bound.

cohorts

A table of cohorts. Each cohort (row) is uniquely identified by the combination of values from the columns: pgs_id, sample_id and cohort_symbol. Columns:

pgs_id

Polygenic Score (PGS) identifier.

sample_id

Sample identifier. This is a surrogate key to identify each sample.

cohort_symbol

Cohort symbol.

cohort_name

Cohort full name.

traits

A table of EFO traits. Each trait (row) is uniquely identified by the combination of the columns pgs_id and efo_id. Columns:

pgs_id

Polygenic Score (PGS) identifier.

efo_id

An EFO identifier.

trait

Trait name.

description

Detailed description of the trait from EFO.

url

External link to the EFO entry.

stages_tally

A table of sample sizes and number of samples sets at each stage.

pgs_id

Polygenic Score (PGS) identifier.

stage

Sample stage: either "gwas", "dev" or "eval".

sample_size

Sample size.

n_sample_sets

Number of sample sets (only meaningful for the evaluation stage "eval")

ancestry_frequencies

This table describes the ancestry composition at each stage.

pgs_id

Polygenic Score (PGS) identifier.

stage

Sample stage: either "gwas", "dev" or "eval".

ancestry_class_symbol

Ancestry class symbol.

frequency

Ancestry fraction (percentage).

multi_ancestry_composition

A table of a breakdown of the ancestries included in multi-ancestries.

pgs_id

Polygenic Score (PGS) identifier.

stage

Sample stage: either "gwas", "dev" or "eval".

multi_ancestry_class_symbol

Multi-ancestry class symbol.

ancestry_class_symbol

Ancestry class symbol.