performance_metrics-class: An S4 class to represent a set of PGS Catalog Performance...
In maialab/quincunx: REST API Client for the 'PGS' Catalog

performance_metrics-class

R Documentation

An S4 class to represent a set of PGS Catalog Performance Metrics

Description

The performance_metrics object consists of nine tables (slots) that combined form a relational database of a subset of performance metrics. Each performance metric is an observation (row) in the scores table (first table).

Slots

performance_metrics

A table of PGS Performance Metrics (PPM). Each PPM (row) is uniquely identified by the ppm_id column. Columns:

ppm_id: A PGS Performance Metrics identifier. Example: "PPM000001".
pgs_id: Polygenic Score (PGS) identifier.
reported_trait: The author-reported trait that the PGS has been developed to predict. Example: "Breast Cancer".
covariates: Comma-separated list of covariates used in the prediction model to evaluate the PGS.
comments: Any other information relevant to the understanding of the performance metrics.

publications

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

ppm_id: A PGS Performance Metrics identifier. Example: "PPM000001".
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 This variable is also curated to allow unpublished work (e.g. preprints) to be added to the catalog.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".

sample_sets

A table of sample sets. Each sample set (row) is uniquely identified by the column pss_id. Columns:

ppm_id: A PGS Performance Metrics identifier. Example: "PPM000001".
pss_id: A PGS Sample Set identifier. Example: "PSS000042".

samples

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

ppm_id: A PGS Performance Metrics identifier. Example: "PPM000001".
pss_id: A PGS Sample Set identifier. Example: "PSS000042".
sample_id: Sample identifier. This is a surrogate key to identify each sample.
stage: Sample stage: should be always Evaluation ("eval").
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: ppm_id, pss_id, sample_id, and variable. Columns:

ppm_id: A PGS Performance Metrics identifier. Example: "PPM000001".
pss_id: A PGS Sample Set identifier. Example: "PSS000042".
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: ppm_id, sample_id and cohort_symbol. Columns:

ppm_id: A PGS Performance Metrics identifier. Example: "PPM000001".
sample_id: Sample identifier. This is a surrogate key to identify each sample.
cohort_symbol: Cohort symbol.
cohort_name: Cohort full name.

pgs_effect_sizes

A table of effect sizes per standard deviation change in PGS. Examples include regression coefficients (betas) for continuous traits, odds ratios (OR) and/or hazard ratios (HR) for dichotomous traits depending on the availability of time-to-event data. Each effect size is uniquely identified by the combination of values from the columns: ppm_id and effect_size_id. Columns:

ppm_id: A PGS Performance Metrics identifier. Example: "PPM000001".
effect_size_id: Effect size identifier. This is a surrogate identifier to identify each effect size.
estimate_type_long: Long notation of the effect size (e.g. Odds Ratio).
estimate_type: Short notation of the effect size (e.g. OR).
estimate: The estimate's value.
unit: Unit of the estimate.
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.

pgs_classification_metrics

A table of classification metrics. Examples include the Area under the Receiver Operating Characteristic (AUROC) or Harrell's C-index (Concordance statistic). Columns:

ppm_id: A PGS Performance Metrics identifier. Example: "PPM000001".
classification_metrics_id: Classification metric identifier. This is a surrogate identifier to identify each classification metric.
estimate_type_long: Long notation of the classification metric (e.g. Concordance Statistic).
estimate_type: Short notation classification metric (e.g. C-index).
estimate: The estimate's value.
unit: Unit of the estimate.
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.

pgs_other_metrics

A table of other metrics that are neither effect sizes nor classification metrics. Examples include: R² (proportion of the variance explained), or reclassification metrics. Columns:

ppm_id: A PGS Performance Metrics identifier. Example: "PPM000001".
other_metrics_id: Other metric identifier. This is a surrogate identifier to identify each metric.
estimate_type_long: Long notation of the metric. Example: "Proportion of the variance explained".
estimate_type: Short notation metric. Example: "R²".
estimate: The estimate's value.
unit: Unit of the estimate.
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.