plot.methytmle {methyvim} | R Documentation |
Plot p-values of methytmle objects
## S3 method for class 'methytmle' plot(x, ..., type = "both")
x |
Object of class |
... |
Additional arguments passed |
type |
The type of plot to build: one of side-by-side histograms (type "both") comparing raw p-values to FDR-adjusted p-values (using the FDR-MSA correction) or either of these two histogram separately. Set this argument to "raw_pvals" for a histogram of the raw p-values, and to "fdr_pvals" for a histogram of the FDR-corrected p-values. |
Object of class ggplot
containing a histogram or side-by-side
histograms of the raw (marginal) and corrected p-values, with the latter
computed automatically using the method of Tuglus and van der Laan.
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" ) ) plot(methyvim_out_ate)