COHCAP (City of Hope CpG Island Analysis Pipeline) is an algorithm to analyze single-nucleotide resolution methylation data (Illumina 450k methylation array, targeted BS-Seq, etc.). It provides QC metrics, differential methylation for CpG Sites, differential methylation for CpG Islands, integration with gene expression data, and visualization of methylation values.
1) COHCAP is undergoing minimal maintenance now, so you may want to consider using other algorithms for your data analysis needs. For example, minfi/bumphunter will be an excellent strategy for most 450k analysis. For example, please see these benchmarks / templates:
2) If you do use COHCAP, it is recommended that you use the Bioconductor version of COHCAP:
- DNA methylation analysis
- integration of methylation and gene expression data
- graphical user interface for basic users
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