sample_sets-class: An S4 class to represent a set of PGS Catalog Sample Sets
In quincunx: REST API Client for the 'PGS' Catalog

sample_sets-class

R Documentation

An S4 class to represent a set of PGS Catalog Sample Sets

Description

The sample_sets object consists of four tables (slots) that combined form a relational database of a subset of PGS Catalog sample sets. Each sample set is an observation (row) in the sample_sets table (first table).

Slots

sample_sets

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

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: pss_id and sample_id. Columns:

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: pss_id, sample_id, and variable. Columns:

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: pss_id, sample_id and cohort_symbol. Columns:

pss_id: A PGS Sample Set identifier. Example: "PSS000042".
sample_id: Sample identifier. This is a surrogate key to identify each sample.
cohort_symbol: Cohort symbol.
cohort_name: Cohort full name.