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| 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"' |