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The phenotype genotype referene map (PGRM)

Source: R/map.R
PGRM_ALL.Rd

This table provides GWAS associations results from the GWAS catalog, annotated by phecodes, ancestry, etc.

Usage

PGRM_ALL

Format

A data.table with the following columns:

  • assoc_ID: Integer vector of the unique identifier for each association

  • SNP_hg19: Character vector variants encoded in hg19 genome reference build

  • SNP_hg38: Character vector variants encoded in hg38 genome reference build

  • rsID: Character indicating the Reference SNP cluster ID

  • risk_allele_dir: Character vector specifying the risk allele direction (alt: Alternate allele, ref: Reference allele)

  • risk_allele: Character specifying the risk allele

  • phecode: Character vector of the phecode for the association

  • phecode_string: Character vector of the phecode string label

  • category_string: Character vector of the phecode category

  • ancestry: Character vector of the ancestery of the source GWAS using 1000 Genomes superpopulations ancestry groupings (AFR: African, EAS: East Asian, EUR: European, AMR: AdMixed American, SAS: South Asian)

  • cat_LOG10_P: Numeric vector of the -log10(P) of the association from the catalog

  • cat_OR: Numeric value of the odds ratio of the association

  • cat_L95: Numeric value of the 95% lower confidence interval of the association

  • cat_U95: Numeric value of the 95% upper confidence interval of the association

  • Study_accession: Character vector of the study accession ID from the GWAS catalog

  • pubmedid: Numeric value of the PubMed ID for source publication of association

  • pub_count: Numeric value indicating how many times association has been published in GWAS catalog

  • first_pub_date: Date of the first date the association was published

  • AFR_RAF: Numeric value of the African ancestry risk allele frequency from gnomAD

  • EUR_RAF: Numeric value of the European (non-Finnish) ancestry risk allele frequency from gnomAD

  • EAS_RAF: Numeric value of the East Asian ancestry risk allele frequency from gnomAD

  • AMR_RAF: Numeric value of the Latino/Admixed American ancestry risk allele frequency from gnomAD

  • SAS_RAF: Numeric value of the South Asian ancestry risk allele frequency from gnomAD

  • ALL_RAF: Numeric value of the risk allele frequency from gnomAD

Source

Allele frequencies: https://gnomad.broadinstitute.org/ Summary statistics: https://www.ebi.ac.uk/gwas/

Details

The odds ratio and 95% confidence intervals (columns cat_OR, cat_L95, and cat_U95) are reported relative to the risk allele which is specified in the column risk_allele.

See also

get_PGRM()