gwascat (version 2.4.2)

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

Description

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

Usage

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

Arguments

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

Value

• autoplot value

Details

uses a ggbio autoplot

Examples

# do a p-value truncation if you want to reduce compression
data(ebicat38)
library(GenomeInfoDb)
seqlevelsStyle(ebicat38) = "UCSC"
traitsManh(ebicat38)