Array Based CpG Region Analysis Pipeline

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Documentation for package ‘ABC.RAP’ version 0.9.0

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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