gwascat-package: representing and modeling data in the NHGRI GWAS catalog

Description

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

Arguments

Details

ll{ 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.

References

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

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

Examples

Run this code

data(ebicat38)
 ebicat38

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