In GenuityScience/topr: Create Custom Plots for Viewing Genetic Association Results

knitr::opts_chunk$set(
  message = FALSE,
  collapse = TRUE,
  comment = "#>"
  )
library(topr)
library(magrittr)
set.seed(0)

When using the regular manhattan function, the user can specify a P-value threshold to highlight significant associations. However, sometimes it is useful to highlight variants using both a genome-wide significant threshold and a suggestive threshold. A good use case for this could be an under powered study with a small sample size. The manhattanExtra extension of manhattan allows the user to easily do this.

There are no additional required arguments for this function, as shown below.

manhattanExtra(CD_UKBB)

The manhattanExtra function can be customized using some of its optional arguments, including genome_wide_thresh, suggestive_thresh, flank_size & region_size. The flank_size parameter is used to denote the size on either side of a top hit that will be included in the colored grouping for that hit. The region_size parameter is used for gene annotation and will determine how dense the labeling is. Larger numbers will have sparser annotations.

Adjusting flank and region sizes -

manhattanExtra(
  CD_UKBB,
  flank_size = 1e6,
  region_size = 1e6
)

manhattanExtra(
  CD_UKBB,
  flank_size = 1e6,
  region_size = 1e8
)

For arguments sake, we can make the thresholds much stricter to see the results -

manhattanExtra(
  CD_UKBB,
  genome_wide_thresh = 1e-12,
  suggestive_thresh = 1e-8
)

manhattanExtra(
  CD_UKBB,
  genome_wide_thresh = 1e-12,
  suggestive_thresh = 1e-8,
  flank_size = 1e6,
  region_size = 1e8
)

GenuityScience/topr documentation built on Oct. 20, 2024, 10:23 p.m.