annot: Query analysis, variant, gene etc. annotation

In tobyjohnson/gtx: Genetics ToolboX

Description

Common queries of the annotation tables of the GWAS summary statistics.

Usage

annot(analysis, chrom, pos, ref, alt, rs, hgnc, ensg, max_variants = 30L,
  max_genes = 3L, dbc = getOption("gtx.dbConnection", NULL))

Arguments

analysis	Analysis identifier
chrom	Chromosome identifier (string)
pos	Position
ref	Reference allele
alt	Alternate allele
rs	dbSNP identifier (e.g. "rs123456")
hgnc	HGNC gene symbol
ensg	Ensembl gene identifier (e.g. "ENSG00000123456")
max_variants	Maximum number of variants to return
max_genes	Maximum number of genes to return
dbc	Database connection (see gtxconnect)

Details

All the main function arguments are optional, but at least one argument must be given in order to generate any results.

Value

Query results

Author(s)

Toby Johnson [e-mail]

tobyjohnson/gtx documentation built on Aug. 30, 2019, 8:07 p.m.