plot.summary.bvs: Plots for Top Variant and Region Inclusions

In USCbiostats/bvs: Bayesian Variable Selection

Description

This function allows the user to create image plots of the top variants and top Regions (any user specified set of variants such as pathways or genes) included in the top models. Variants and Regions are ordered based on marginal BF and regional BF which are plotted on the right axis. The width of the inclusion blocks are proportional to the posterior model probability that the variant or region is included in.

Usage

## S3 method for class 'summary.bvs'
plot(x, type = c("s", "r"), num_models = 100,
  num_snps = 20, num_regions = 20, plot_coef = FALSE, true_coef = NULL,
  regions = NULL, prop_cases = NULL, main = NULL, ...)

Arguments

x	an object of class 'summary.bvs'
type	specifies whether to plot the top variants ("s") or the top regions ("r")
num_models	the number of top models to place on the x-axis
num_snps	if type = "s", the number of the top variants to place on the y-axis
num_regions	if type = "r", the number ofthe top regions to place on the y-axis
plot_coef	only used for rare variant analysis when rare = TRUE and there are not multiple regions. If plot_coef = TRUE, the log(OR) of the risk index for the top models is plotted on the x-axis
true_coef	(optional) vector of the true odds ratios of each of the variants to plot on the y-axis (i.e. if results are from a simulation)
regions	(optional) string vector with the region name for each of the variants. By default, region names are used from the 'summary.bvs' x. Using this argument will overwrite the names in the "summary.bvs" x.
prop_cases	(optional) p x 2 matrix giving the number of cases that have the variant in column 1 and the number of controls with the variant in column 2. If specified, these counts will be reported on the right axis under each variants marginal BF.
main	optional string variable giving the title of the plot
...	additional arguments as required by plot S3 x

USCbiostats/bvs documentation built on April 30, 2021, 12:29 a.m.