methyvolc {methyvim}R Documentation

Volcano plot for methytmle objects

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])
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)

[Package methyvim version 1.2.0 Index]