ABC.RAP (version 0.9.0)

plot_data: Overview description of the DNA methylation pattern for cases and controls

Description

This function produces four distribution plots that summarise the DNA methylation patterns for cases (top left) and controls (top right). The top two histograms show the pattern of mean DNA methylation levels for cases and controls. The bottom two plots show the difference in DNA methylation between cases and controls (a boxplot comparing methylation profile for cases and controls, and a delta beta plot describing the methylation difference between cases and controls). The function also provides summary statistics for the delta beta analysis that can be used to select cutoff values for the delta_beta_data function.

Usage

plot_data(x, cases_column_1, cases_column_n, controls_column_1, controls_column_n)

Arguments

x

The filtered 450k probes from filter_data() function

cases_column_1

The first column (column number) for cases in the filtered dataset

cases_column_n

The last column (column number) for cases in the filtered dataset

controls_column_1

The first column (column number) for controls in the filtered dataset

controls_column_n

The last column (column number) for controls in the filtered dataset

Examples

data(test_data)
data(nonspecific_probes)
test_data_filtered <- filter_data(test_data)
plot_data(test_data_filtered, 1, 2, 3, 4)