ABC.RAP (version 0.9.0)

Array Based CpG Region Analysis Pipeline

Description

It aims to identify candidate genes that are “differentially methylated” between cases and controls. It applies Student’s t-test and delta beta analysis to identify candidate genes containing multiple “CpG sites”.

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Version

Install

install.packages('ABC.RAP')

Monthly Downloads

315

Version

0.9.0

License

GPL-3

Maintainer

Abdulmonem Alsaleh

Last Published

October 20th, 2016

Functions in ABC.RAP (0.9.0)

plot_data

Overview description of the DNA methylation pattern for cases and controls

ttest_data

applying t-test analysis

process.ABC.RAP

An automated analysis applying all ABC.RAP functions in one script

test_data

test dataset of 450k DNA methylation

CpG_hits

Identifying genes for which multiple CpG sites show significant methylation difference

annotate_data

Annotating the filtered probes

overlap_data

Overlapping Student's t-test and delta beta results

filter_data

Filtering DNA methylation 450k non_specific probes

plot_gene

Plotting and exporting methylation profile for candidate genes

annotation_file

annotation file for the 450k probes

delta_beta_data

Applying delta beta analysis to calculate the difference between cases and controls

nonspecific_probes

450k DNA methylation non specific probes

plot_candidate_genes

Plotting highly different and significant probes annotated by their corresponding gene names