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::IRanges(start = 37500000, width =
        1e+06)),
      txrefobj = TxDb.Hsapiens.UCSC.hg19.knownGene::TxDb.Hsapiens.UCSC.hg19.knownGene,
      genome = "hg19",
      genesymobj = org.Hs.eg.db::org.Hs.eg.db,
      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
`txrefobj` | a TxDb instance
`genome` | character tag like 'hg19'
`genesymobj` | an OrgDb instance
`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

     data(ebicat_2020_04_30)
     # GenomeInfoDb::seqlevelsStyle(ebicat_2020_04_30) = "UCSC" # no more
     GenomeInfoDb::seqlevels(ebicat_2020_04_30) = paste0("chr", GenomeInfoDb::seqlevels(ebicat_2020_04_30))
     gwcex2gviz(ebicat_2020_04_30)

[Package gwascat version 2.24.0 Index]