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

## Documentation for package ‘gwascat’ version 2.38.0

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

## Help Pages

as_GRanges | produce a GRanges from gwascat tibble
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
ebicat_2020_04_30 | serialized gwaswloc instance from april 30 2020, sample of 50000 records
efo.obo.g | convert a typical OBO text file to a graphNEL instance (using Term elements)
g17SM | SnpMatrix instance from chr17
getRsids | generic snp name retrieval
getRsids-method | specific snp name retrieval
getTraits | generic trait retrieval
getTraits-method | specific trait retrieval
get_cached_gwascat | use BiocFileCache to retrieve and keep an image of the tsv file distributed by EBI
gg17N | genotype matrix from chr17 1000 genomes
gr6.0_hg38 | image of locon6 in GRanges, lifted over to hg38
gw6.rs_17 | character vector of rs numbers for SNP on chr17
gwascat_from_AHub | grab an image of EBI GWAS catalog from AnnotationHub
gwastagger | GRanges with LD information on 9998 SNP
gwaswloc-class | container for gwas hit data and GRanges for addresses
gwcat_snapshot | use AnnotationHub snapshot as basis for gwaswloc structure creation
gwcex2gviz | Prepare salient components of GWAS catalog for rendering with Gviz
ldtagr | expand a list of variants by including those in a VCF with LD exceeding some threshold; uses snpStats ld()
locon6 | location data for 10000 SNP
locs4trait | get locations for SNP affecting a selected trait
low17 | SnpMatrix instance from chr17

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)
process_gwas_dataframe | convert GWAS catalog data.frame to gwaswloc, a GRanges extension with simple show method
riskyAlleleCount | given a matrix of subjects x SNP calls, count number of risky alleles
si.hs.37 | Seqinfo for GRCh37
si.hs.38 | Seqinfo for GRCh38
subsetByChromosome | generic trait subsetting
subsetByChromosome-method | specific trait subsetting
subsetByTraits | generic trait subsetting
subsetByTraits-method | specific trait subsetting
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 | extractor for gwaswloc