methyvolc: Volcano plot for methytmle objects

In nhejazi/methyvim: Targeted, Robust, and Model-free Differential Methylation Analysis

Description

Volcano plot for methytmle objects

Usage

methyvolc(x, param_bound = 2, pval_bound = 0.2)

Arguments

x	Object of class methytmle as produced by an appropriate call to methyvim.
param_bound	Numeric for a threshold indicating the magnitude of the size of the effect considered to be interesting. This is used to assign groupings and colors to individual CpG sites.
pval_bound	Numeric for a threshold indicating the magnitude of p-values deemed to be interesting. This is used to assign groupings and colors to individual CpG sites.

Value

Object of class ggplot containing a volcano plot of the estimated effect size on the x-axis and the -log10(p-value) on the y-axis. The volcano plot is used to detect possibly false positive cases, where a test statistic is significant due to low variance.

Examples

suppressMessages(library(SummarizedExperiment))
library(methyvimData)
data(grsExample)
var_int <- as.numeric(colData(grsExample)[, 1])
# TMLE procedure for the ATE parameter over M-values with Limma filtering
methyvim_out_ate <- suppressWarnings(
  methyvim(
    data_grs = grsExample, sites_comp = 25, var_int = var_int,
    vim = "ate", type = "Mval", filter = "limma", filter_cutoff = 0.1,
    parallel = FALSE, tmle_type = "glm"
  )
)
methyvolc(methyvim_out_ate)

nhejazi/methyvim documentation built on April 30, 2020, 7:14 p.m.