Description Usage Arguments Examples
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.
1 2 | plot_gene(x, b, cases_column_1, cases_column_n, controls_column_1,
controls_column_n)
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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 |
1 2 3 4 5 6 7 |
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)
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