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gwascat (version 2.4.2)

representing and modeling data in the EMBL-EBI GWAS catalog

Description

Represent and model data in the EMBL-EBI GWAS catalog.

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Version

Version

2.4.2

License

Artistic-2.0

Maintainer

Vince Carey

Last Published

February 15th, 2017

Functions in gwascat (2.4.2)

gwcex2gviz

Prepare salient components of GWAS catalog for rendering with Gviz
gwascat-package

representing and modeling data in the NHGRI GWAS catalog
gwaswloc-class

Class "gwaswloc"
traitsManh

use ggbio facilities to display GWAS results for selected traits in genomic coordinates
topTraits

operations on GWAS catalog
ldtagr

expand a list of variants by including those in a VCF with LD exceeding some threshold
gwastagger

data on 1000 genomes SNPs that 'tag' GWAS catalog entries
gwdf_2012_02_02

internal data frame for NHGRI GWAS catalog
riskyAlleleCount

given a matrix of subjects x SNP calls, count number of risky alleles
makeCurrentGwascat

read NHGRI GWAS catalog table and construct associated GRanges instance
obo2graphNEL

convert a typical OBO text file to a graphNEL instance (using Term elements)
bindcadd_snv

bind CADD scores of Kircher et al. 2014 to a GRanges instance
locon6

location information for 10000 SNPs probed on Affy GW 6.0