plot_gene: Plotting and exporting methylation profile for candidate...

Description Usage Arguments Examples

View source: R/plot_gene.R

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<e2><80><99> to 3<e2><80><99> 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

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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

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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)

ABC.RAP documentation built on May 2, 2019, 9:16 a.m.