gwascat (version 2.4.2)

gwcex2gviz: Prepare salient components of GWAS catalog for rendering with Gviz

Description

Prepare salient components of GWAS catalog for rendering with Gviz

Usage

gwcex2gviz(basegr, contextGR = GRanges(seqnames =
                 "chr17", IRanges(start = 37500000, width = 1e+06)),
                 txrefpk = "TxDb.Hsapiens.UCSC.hg19.knownGene", genome
                 = "hg19", genesympk = "Homo.sapiens", plot.it = TRUE,
                 maxmlp = 25)

Arguments

basegr

gwaswloc instance containing information about GWAS in catalog

contextGR

A GRanges instance delimiting the visualization in genomic coordinates

txrefpk

a TxDb package, typically

genesympk

string naming annotationDbi .db package

genome

character tag like 'hg19'

plot.it

logical, if FALSE, just return list

maxmlp

maximum value of -10 log p -- winsorization of all larger values is performed, modifying the contents of Pvalue_mlogp in the elementMetadata for the call

Examples

args(gwcex2gviz)
#gwascat:::.onAttach("", "gwascat")
data(ebicat37)
seqlevelsStyle(ebicat37) = "UCSC"
gwcex2gviz(ebicat37)