makeCurrentGwascat {gwascat} | R Documentation

## 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

### 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

    ## Not run:
    # if you have good internet access
    newcatr = makeCurrentGwascat()

    ## End(Not run)

[Package gwascat version 2.12.0 Index]