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

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Documentation for package ‘COHCAP’ version 1.46.0

• 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