COHCAP.denovo {COHCAP} | R Documentation

## De-Novo Identification of Differentially Methylated CpG Site Clusters

### Description

Identifies differentially methylated CpG sites that form clusters.

Only works with 2-group comparison result. Does not map regions to genes or integrate with gene expression data.

### Usage

    COHCAP.denovo(site.table, project.name, project.folder,
    				min.sites = 4, max.dist = 500, output.format = "txt")

### Arguments

`site.table` | Data frame with CpG site statistics (one row per CpG site) and CpG site annotations (in columns 2-5). The COHCAP.site function automatically creates this file.
`project.name` | Name for COHCAP project. This determines the names for output files.
`project.folder` | Folder for COHCAP output files.
`min.sites` | Minimum number of differentially methylated sites to define a differentially methylated CpG island.
`max.dist` | Maximum distance between ordered differentially methylated CpG sites to be considered in a cluster.
`output.format` | Format for output tables: 'xls' for Excel file, 'csv' for comma-separated file, or 'txt' for tab-delimited text file.

### Value

Returns a table of clusters of differentially methylated sites, defined using criteria specified to COHCAP.site()

### See Also

COHCAP Discussion Group: http://sourceforge.net/p/cohcap/discussion/general/

### Examples

    library("COHCAP")

    dir = system.file("extdata", package="COHCAP")
    beta.file = file.path(dir,"GSE42308_truncated.txt")
    sample.file = file.path(dir,"sample_GSE42308.txt")
    project.folder = tempdir()#you may want to use getwd() or specify another folder
    project.name = "450k_test"

    beta.table = COHCAP.annotate(beta.file, project.name, project.folder,
    				platform="450k-UCSC")
    filtered.sites = COHCAP.site(sample.file, beta.table, project.name,
    				project.folder, ref="parental")
    COHCAP.denovo(filtered.sites, project.name, project.folder)

[Package COHCAP version 1.34.1 Index]