makeCurrentGwascat: read NHGRI GWAS catalog table and construct associated...

In vjcitn/gwascat: representing and modeling data in the EMBL-EBI GWAS catalog

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

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.

Value

a GRanges instance

Author(s)

VJ Carey

Examples

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

vjcitn/gwascat documentation built on May 5, 2019, 7:59 p.m.