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 2.24.0 Index]