gwascat: representing and modeling data in the EMBL-EBI GWAS catalog

Represent and model data in the EMBL-EBI GWAS catalog.

Author
VJ Carey <stvjc@channing.harvard.edu>
Date of publication
None
Maintainer
VJ Carey <stvjc@channing.harvard.edu>
License
Artistic-2.0
Version
2.6.0

View on Bioconductor

Man pages

bindcadd_snv
bind CADD scores of Kircher et al. 2014 to a GRanges instance
gwascat-package
representing and modeling data in the NHGRI GWAS catalog
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...
gwdf_2012_02_02
internal data frame for NHGRI GWAS catalog
ldtagr
expand a list of variants by including those in a VCF with LD...
locon6
location information for 10000 SNPs probed on Affy GW 6.0
makeCurrentGwascat
read NHGRI GWAS catalog table and construct associated...
obo2graphNEL
convert a typical OBO text file to a graphNEL instance (using...
riskyAlleleCount
given a matrix of subjects x SNP calls, count number of risky...
topTraits
operations on GWAS catalog
traitsManh
use ggbio facilities to display GWAS results for selected...

Files in this package

gwascat/DESCRIPTION
gwascat/NAMESPACE
gwascat/NEWS
gwascat/R
gwascat/R/addSeqlengths.R
gwascat/R/bindcadd_snv.R
gwascat/R/classes.R
gwascat/R/descendants.R
gwascat/R/ebiquery.R
gwascat/R/fixnonasc.R
gwascat/R/funcs.R
gwascat/R/gwcex2gviz.R
gwascat/R/ldtagr.R
gwascat/R/makeConsecChrs.R
gwascat/R/obotools.R
gwascat/R/traitsManh.R
gwascat/R/updater.R
gwascat/R/zzz.R
gwascat/build
gwascat/build/vignette.rds
gwascat/data
gwascat/data/datalist
gwascat/data/ebicat37.rda
gwascat/data/ebicat37UCSC.rda
gwascat/data/ebicat38.rda
gwascat/data/efo.obo.g.rda
gwascat/data/g17SM.rda
gwascat/data/gg17N.rda
gwascat/data/gw6.rs_17.rda
gwascat/data/gwastagger.rda
gwascat/data/gwdf_2014_09_08.rda
gwascat/data/gwrngs19.rda
gwascat/data/gwrngs38.rda
gwascat/data/locon6.rda
gwascat/data/low17.rda
gwascat/data/rules_6.0_1kg_17.rda
gwascat/data/si.hs.37.rda
gwascat/data/si.hs.38.rda
gwascat/inst
gwascat/inst/csv
gwascat/inst/csv/nomatch.csv
gwascat/inst/doc
gwascat/inst/doc/gwascat.R
gwascat/inst/doc/gwascat.Rnw
gwascat/inst/doc/gwascat.pdf
gwascat/inst/doc/gwascatOnt.R
gwascat/inst/doc/gwascatOnt.Rmd
gwascat/inst/doc/gwascatOnt.html
gwascat/inst/gff3
gwascat/inst/gff3/chr17_34834101_35834100.gff3
gwascat/inst/gff3/chr17_43000000_45000000.gff3
gwascat/inst/obo
gwascat/inst/obo/HumanDO.obo.gz
gwascat/inst/obo/efo.020815.obo.gz
gwascat/inst/obo/hpo.obo.gz
gwascat/inst/olddata
gwascat/inst/olddata/gwdf_2012_03_20.rda
gwascat/inst/olddata/gwdf_2012_09_22.rda
gwascat/inst/olddata/gwrngs.rda
gwascat/inst/scripts
gwascat/inst/scripts/builders.hist.txt
gwascat/inst/scripts/doebicat38.hist.txt
gwascat/inst/tab
gwascat/inst/tab/build0307df.hist.txt
gwascat/inst/tab/build0307df.hist.txt.gz
gwascat/inst/tab/gwascatalog20120307.txt.gz
gwascat/inst/tab/gwascatalog20120320.txt.gz
gwascat/inst/tab/import_gwtab.R
gwascat/inst/unitTests
gwascat/inst/unitTests/test_gwascat.R
gwascat/man
gwascat/man/bindcadd_snv.Rd
gwascat/man/gwascat-package.Rd
gwascat/man/gwastagger.Rd
gwascat/man/gwaswloc-class.Rd
gwascat/man/gwcex2gviz.Rd
gwascat/man/gwdf_2012_02_02.Rd
gwascat/man/ldtagr.Rd
gwascat/man/locon6.Rd
gwascat/man/makeCurrentGwascat.Rd
gwascat/man/obo2graphNEL.Rd
gwascat/man/riskyAlleleCount.Rd
gwascat/man/topTraits.Rd
gwascat/man/traitsManh.Rd
gwascat/tests
gwascat/tests/test-all.R
gwascat/vignettes
gwascat/vignettes/gwascat.Rnw
gwascat/vignettes/gwascat.bib
gwascat/vignettes/gwascatOnt.Rmd
gwascat/vignettes/litman.pdf