makeCurrentGwascat {gwascat} | R Documentation

## read NHGRI GWAS catalog table and construct associated GRanges instance 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.

### Description

read NHGRI GWAS catalog table and construct associated GRanges instance 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.

### 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

### Author(s)

VJ Carey

### Examples

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

[Package gwascat version 2.20.1 Index]