# CpG Island Analysis Pipeline for Illumina Methylation Array and Targeted BS-Seq Data

## Documentation for package ‘COHCAP’ version 1.40.0

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

## Help Pages

COHCAP.annotate | Annotation for CpG Sites
COHCAP.avg.by.island | CpG Island Differential Methylation Analysis (Average by Island Workflow).
COHCAP.avg.by.site | CpG Island Differential Methylation Analysis (Average by Site Workflow).
COHCAP.BSSeq.preprocess | Preprocessing for Targeted BS-Seq data
COHCAP.BSSeq_V2.methyl.table | Create Percent Methylation Table from Bismark Coverage files for Targeted BS-Seq data
COHCAP.denovo | De-Novo Identification of Differentially Methylated CpG Site Clusters
COHCAP.integrate.avg.by.island | Integration with Gene Expression Data(Average by Island Workflow).
COHCAP.integrate.avg.by.site | Integration with Gene Expression Data(Average by Site Workflow).
COHCAP.qc | DNA Methylation Quality Control Statistics
COHCAP.reformatFinalReport | Prepare COHCAP beta file from Illumina GenomeStudio Final Report
COHCAP.site | CpG Site Differential Methylation Analysis