# Array Based CpG Region Analysis Pipeline

## Documentation for package ‘ABC.RAP’ version 0.9.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

annotate_data | Annotating the filtered probes
annotation_file | annotation file for the 450k probes
CpG_hits | Identifying genes for which multiple CpG sites show significant methylation difference
delta_beta_data | Applying delta beta analysis to calculate the difference between cases and controls
filter_data | Filtering DNA methylation 450k non_specific probes
nonspecific_probes | 450k DNA methylation non specific probes
overlap_data | Overlapping Student's t-test and delta beta results
plot_candidate_genes | Plotting highly different and significant probes annotated by their corresponding gene names
plot_data | Overview description of the DNA methylation pattern for cases and controls
plot_gene | Plotting and exporting methylation profile for candidate genes
process.ABC.RAP | An automated analysis applying all ABC.RAP functions in one script
test_data | test dataset of 450k DNA methylation
ttest_data | applying t-test analysis