traitsManh {gwascat}R Documentation

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

Details

uses a ggbio autoplot

Value

autoplot value

Note

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

Author(s)

VJ Carey <stvjc@channing.harvard.edu>

Examples


# 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)


[Package gwascat version 2.26.0 Index]