gwcex2gviz {gwascat} | R Documentation

## 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)

[Package gwascat version 2.16.1 Index]