gwascat (version 2.4.2)

makeCurrentGwascat: read NHGRI GWAS catalog table and construct associated GRanges instance

Description

read NHGRI table and construct associated GRanges instance

Usage

makeCurrentGwascat(table.url =
                 "http://www.ebi.ac.uk/gwas/api/search/downloads/alternative",
                 fixNonASCII = TRUE, genome="GRCh38",
                 withOnt = TRUE)

Arguments

table.url

string identifying the .txt file curated at EBI/EMBL

fixNonASCII

logical, if TRUE, non-ASCII characters as identified by iconv will be replaced by asterisk

genome

character string: 'GRCh38' is default and yields current image as provided by EMBL/EBI; 'GRCh37' yields a realtime liftOver to hg19 coordinates, via AnnotationHub storage of the chain files. Any other value yields an error.

withOnt

logical indicating whether 'alternative' (ontology-present, includes repetition of loci with one:many ontological mapping) or 'full' (ontology-absent, one record per locus report) version of distributed table

Value

• a GRanges instance

Details

records for which clear genomic position cannot be determined are dropped from the ranges instance

an effort is made to use reasonable data types for GRanges metadata, so some qualifying characters such as (EA) in Risk allele frequency field will simply be omitted during coercion of contents of that field to numeric.

Examples

# if you have good internet access
newcatr = makeCurrentGwascat()