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

## Documentation for package ‘gwascat’ version 2.20.1

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

## Help Pages

gwascat-package | representing and modeling data in the NHGRI GWAS catalog, using GRanges and allied infrastructure
bindcadd_snv | bind CADD scores of Kircher et al. 2014 to a GRanges instance
chklocs | return TRUE if all named SNPs with locations in both the SNPlocs package and the gwascat agree
DataFrame | representing and modeling data in the NHGRI GWAS catalog, using GRanges and allied infrastructure
ebicat37 | a legacy representation of EBI's GWAS catalog with loci annotated to positions on GRCh37
ebicat37UCSC | a legacy representation of EBI's GWAS catalog with loci annotated to positions on GRCh37 but UCSC chromosome names
ebicat38 | representing and modeling data in the NHGRI GWAS catalog, using GRanges and allied infrastructure
ebicat_b37 | a legacy representation of EBI's GWAS catalog with loci annotated to positions on GRCh37
ebicat_b38 | a legacy representation of EBI's GWAS catalog with loci annotated to positions on GRCh38
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, using GRanges and allied infrastructure
getRsids | Class '"gwaswloc"'
getRsids-method | Class '"gwaswloc"'
getTraits | Class '"gwaswloc"'
getTraits-method | Class '"gwaswloc"'
gg17N | representing and modeling data in the NHGRI GWAS catalog, using GRanges and allied infrastructure
gw6.rs_17 | representing and modeling data in the NHGRI GWAS catalog, using GRanges and allied infrastructure
gwascat | representing and modeling data in the NHGRI GWAS catalog, using GRanges and allied infrastructure
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_2012_02_02 | internal data frame for NHGRI GWAS catalog
gwdf_2014_09_08 | internal data frame for NHGRI GWAS catalog
gwrngs19 | representing and modeling data in the NHGRI GWAS catalog, using GRanges and allied infrastructure
gwrngs38 | representing and modeling data in the NHGRI GWAS catalog, using GRanges and allied infrastructure
impute.snps | representing and modeling data in the NHGRI GWAS catalog, using GRanges and allied infrastructure
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 | get locations for SNP affecting a selected trait
low17 | representing and modeling data in the NHGRI GWAS catalog, using GRanges and allied infrastructure
makeCurrentGwascat | 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.
node2uri | convert a typical OBO text file to a graphNEL instance (using Term elements)
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, using GRanges and allied infrastructure
show-method | Class '"gwaswloc"'
si.hs.37 | seqinfo for GRCh37
si.hs.38 | representing and modeling data in the NHGRI GWAS catalog, using GRanges and allied infrastructure
SnpMatrix-class | representing and modeling data in the NHGRI GWAS catalog, using GRanges and allied infrastructure
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
uri2node | convert a typical OBO text file to a graphNEL instance (using Term elements)
[-method | Class '"gwaswloc"'