COHCAP.denovo: De-Novo Identification of Differentially Methylated CpG Site...

In cwarden45/COHCAP: CpG Island Analysis Pipeline for Illumina Methylation Array and Targeted BS-Seq Data

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)

cwarden45/COHCAP documentation built on April 16, 2024, 3:17 a.m.