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

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

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)

gwascat documentation built on Nov. 8, 2020, 11:08 p.m.