gwcex2gviz {gwascat} | R Documentation |
Prepare salient components of GWAS catalog for rendering with Gviz
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 )
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 |
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)