methyvolc {methyvim} | R Documentation |
Volcano plot for methytmle objects
methyvolc(x, param_bound = 2, pval_bound = 0.2)
x |
Object of class |
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. |
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.
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)