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| 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 |
| 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 |