methyvolc: Volcano plot for methytmle objects

Description Usage Arguments Value Examples

View source: R/plots.R

Description

Volcano plot for methytmle objects

Usage

1
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

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
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)

methyvim documentation built on Nov. 8, 2020, 11:11 p.m.