Man pages for gwascat
representing and modeling data in the EMBL-EBI GWAS catalog
| 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... |
| ebicat_2020_04_30 | serialized gwaswloc instance from april 30 2020, sample of... |
| g17SM | SnpMatrix instance from chr17 |
| get_cached_gwascat | use BiocFileCache to retrieve and keep an image of the tsv... |
| getRsids | generic snp name retrieval |
| getRsids-gwaswloc-method | specific snp name retrieval |
| getTraits | generic trait retrieval |
| getTraits-gwaswloc-method | specific trait retrieval |
| 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 |
| gwastagger | GRanges with LD information on 9998 SNP |
| gwaswloc-class | container for gwas hit data and GRanges for addresses |
| gwcex2gviz | Prepare salient components of GWAS catalog for rendering with... |
| ldtagr | expand a list of variants by including those in a VCF with 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... |
| obo2graphNEL | convert a typical OBO text file to a graphNEL instance (using... |
| process_gwas_dataframe | convert GWAS catalog data.frame to gwaswloc, a GRanges... |
| riskyAlleleCount | given a matrix of subjects x SNP calls, count number of risky... |
| si.hs.37 | Seqinfo for GRCh37 |
| si.hs.38 | Seqinfo for GRCh38 |
| sub-gwaswloc-ANY-ANY-ANY-method | extractor for gwaswloc |
| subsetByChromosome | generic trait subsetting |
| subsetByChromosome-gwaswloc-method | specific trait subsetting |
| subsetByTraits | generic trait subsetting |
| subsetByTraits-gwaswloc-method | specific trait subsetting |
| topTraits | operations on GWAS catalog |
| traitsManh | use ggbio facilities to display GWAS results for selected... |
