ABC.RAP (version 0.9.0)

plot_gene: Plotting and exporting methylation profile for candidate genes

Description

This function explores the DNA methylation profile for any gene. The function generates four plots: the top plots show the difference in DNA methylation between cases and controls (a bar chart of the delta beta values for all probes arranged from 5’ to 3’ positions and a plot showing the difference in mean DNA methylation between cases and controls). The bottom plots show the distribution of DNA methylation for each probe that interrogates a CpG site in the investigated gene, for cases (left) and controls (right), respectively. Also, an annotation table for the arranged probes is generated with the following columns: probe names, gene name, distance from TSS, mean methylation for cases, mean methylation for controls, delta beta values (cases minus controls), and t-test p.values.

Usage

plot_gene(x, b, cases_column_1, cases_column_n, controls_column_1, controls_column_n)

Arguments

x

The filtered and annotated 450k probes

b

Gene name between quotation marks

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)
data(annotation_file)
test_data_filtered <- filter_data(test_data)
test_data_annotated <- annotate_data(test_data_filtered)
KLHL34 <- plot_gene(test_data_annotated, 'KLHL34', 1, 2, 3, 4)