# representing and modeling data in the EMBL-EBI GWAS catalog

## Documentation for package ‘gwascat’ version 2.6.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

gwascat-package | representing and modeling data in the NHGRI GWAS catalog
adj | representing and modeling data in the NHGRI GWAS catalog
bindcadd_snv | bind CADD scores of Kircher et al. 2014 to a GRanges instance
chklocs | operations on GWAS catalog
DataFrame | representing and modeling data in the NHGRI GWAS catalog
ebicat37 | representing and modeling data in the NHGRI GWAS catalog
ebicat38 | representing and modeling data in the NHGRI GWAS catalog
efo.obo.g | convert a typical OBO text file to a graphNEL instance (using Term elements)
g17SM | representing and modeling data in the NHGRI GWAS catalog
getRsids | Class '"gwaswloc"'
getRsids-method | Class '"gwaswloc"'
getTraits | Class '"gwaswloc"'
getTraits-method | Class '"gwaswloc"'
gg17N | representing and modeling data in the NHGRI GWAS catalog
gw6.rs_17 | representing and modeling data in the NHGRI GWAS catalog
gwascat | representing and modeling data in the NHGRI GWAS catalog
gwastagger | data on 1000 genomes SNPs that 'tag' GWAS catalog entries
gwaswloc-class | Class '"gwaswloc"'
gwcex2gviz | Prepare salient components of GWAS catalog for rendering with Gviz
gwdf_2014_09_08 | internal data frame for NHGRI GWAS catalog
gwrngs19 | representing and modeling data in the NHGRI GWAS catalog
gwrngs38 | representing and modeling data in the NHGRI GWAS catalog
impute.snps | representing and modeling data in the NHGRI GWAS catalog
ldtagr | expand a list of variants by including those in a VCF with LD exceeding some threshold
locon6 | location information for 10000 SNPs probed on Affy GW 6.0
locs4trait | operations on GWAS catalog
low17 | representing and modeling data in the NHGRI GWAS catalog
makeCurrentGwascat | read NHGRI GWAS catalog table and construct associated GRanges instance
node2uri | convert a typical OBO text file to a graphNEL instance (using Term elements)
nodeData | representing and modeling data in the NHGRI GWAS catalog
nodes | representing and modeling data in the NHGRI GWAS catalog
obo2graphNEL | convert a typical OBO text file to a graphNEL instance (using Term elements)
riskyAlleleCount | given a matrix of subjects x SNP calls, count number of risky alleles
rules_6.0_1kg_17 | representing and modeling data in the NHGRI GWAS catalog
show-method | Class '"gwaswloc"'
si.hs.38 | representing and modeling data in the NHGRI GWAS catalog
SnpMatrix-class | representing and modeling data in the NHGRI GWAS catalog
subGraph | representing and modeling data in the NHGRI GWAS catalog
subsetByChromosome | Class '"gwaswloc"'
subsetByChromosome-method | Class '"gwaswloc"'
subsetByTraits | Class '"gwaswloc"'
subsetByTraits-method | Class '"gwaswloc"'
topTraits | operations on GWAS catalog
traitsManh | use ggbio facilities to display GWAS results for selected traits in genomic coordinates
ugraph | representing and modeling data in the NHGRI GWAS catalog
uri2node | convert a typical OBO text file to a graphNEL instance (using Term elements)
[-method | Class '"gwaswloc"'