gwascat-package {gwascat} | R Documentation

## representing and modeling data in the NHGRI GWAS catalog

### Description

representing and modeling data in the NHGRI GWAS catalog, using GRanges and allied infrastructure

### Details

Package: | gwascat
Version: | 1.7.3
Suggests: |
Depends: | R (>= 3.0.0), methods, IRanges, GenomicRanges
Imports: |
License: | Artistic-2.0
LazyLoad: | yes

Index:

    gwaswloc-class          Class '"gwaswloc"'

The GWAS catalog management has migrated to EMBL/EBI. Use data(ebicat38) for an image dated 3 August 2015. Use makeCurrentGwascat() to get a more recent image. Use data(ebicat37) for a GRCh37 (or hg19) liftOver result. Use data(ebicat37UCSC) for an image with `hg19` as genome tag and UCSC seqnames.

The data objects

'g17SM' 'gg17N' 'gw6.rs_17' 'low17' 'rules_6.0_1kg_17' 'gwrngs'

are described in vignettes.

The DataFrame function is imported from IRanges.

The `SnpMatrix-class` is used to represent data related to rule-based imputation, using the `impute.snps` function.

si.hs.38 is a `Seqinfo-class` instance for hg38.

`nodeData` (and nodes, ugraph, subGraph, adj) are exported for use in the vignettes.

### Author(s)

VJ Carey <stvjc@channing.harvard.edu>

Maintainer: VJ Carey <stvjc@channing.harvard.edu>

### References

http://www.genome.gov/gwastudies/.

Partial support from the Computational Biology Group at Genentech, Inc.

### Examples

    ## Not run:
     data(ebicat38)
     ebicat38

    ## End(Not run)

[Package gwascat version 2.12.0 Index]