traitsManh: use ggbio facilities to display GWAS results for selected...
In gwascat: representing and modeling data in the EMBL-EBI GWAS catalog

Description Usage Arguments Details Value Note Author(s) Examples

use ggbio facilities to display GWAS results for selected traits in genomic coordinates

traitsManh(
  gwr,
  selr = GRanges(seqnames = "chr17", IRanges(3e+07, 5e+07)),
  traits = c("Asthma", "Parkinson's disease", "Height", "Crohn's disease"),
  truncmlp = 25,
  ...
)

`gwr`	GRanges instance as managed by the gwaswloc container design, with Disease.Trait and Pvalue\_mlog among elementMetadata columns
`selr`	A GRanges instance to restrict the `gwr` for visualization. Not tested for noncontiguous regions.
`traits`	Character vector of traits to be exhibited; GWAS results with traits not among these will be labeled “other”.
`truncmlp`	Maximum value of -log10 p to be displayed; in the raw data this ranges to the hundreds and can cause bad compression.
`...`	not currently used

uses a ggbio autoplot

autoplot value

An xlab is added, concatenating genome tag with seqnames tag.

VJ Carey <stvjc@channing.harvard.edu>

# do a p-value truncation if you want to reduce compression
## Not run:   # ggbio July 2018
data(ebicat_2020_04_30)
library(GenomeInfoDb)
seqlevelsStyle(ebicat_2020_04_30) = "UCSC"
traitsManh(ebicat_2020_04_30)
 
## End(Not run)