representing and modeling data in the EMBL-EBI GWAS catalog


[Up] [Top]

Documentation for package ‘gwascat’ version 2.19.3

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"'