plot_signif_distribs: Plot the distributions of case and control variant residues...

In adamwaring/ClusterBurden: Rare variant association utilising burden and positional information.

Description

Plot the distributions of case and control variant residues across multiple genes

Usage

plot_signif_distribs(
  pvals,
  cases,
  controls,
  case_coverage,
  control_coverage,
  test = "BIN-test",
  cov_threshold = 0.5,
  n_genes = 20,
  SCALE = 1
)

Arguments

pvals	pvals data.table from ClusterBurden WES analysis with at least symbol and p-value column for test of interest
cases	case data in format: data.table(aff, symbol, protein_position, ac)
controls	control data in format: data.table(aff, symbol, protein_position, ac)
case_coverage	optional coverage data for cases in format: data.table(symbol, protein_position, over_10)
control_coverage	optional coverage data for controls in format: data.table(symbol, protein_position, over_10)
test	either bin-test, burden or clusterburden (not case sensitive)
cov_threshold	threshold at which to exclude a residue position from the analysis (choose 0 to keep all residues)
n_genes	number of genes to plot e.g. n_genes = 5 plots the 5 most significant genes
SCALE	scale of the plot

Details

For each gene (n_genes=?): produces a stripchart using geom_jitter for both cases and controls as well as a gaussian density line for each cohort. If coverage files are provided then these are included as a rug underneath and above the case and control variants and are colored by their coverage level (< cov_threshold, < 80

Value

Returns a ggplot object

Author(s)

Adam Waring - [e-mail]

adamwaring/ClusterBurden documentation built on July 29, 2020, 9:50 p.m.