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

Description Usage Arguments Value See Also Examples

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

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

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

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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 <- getwd()
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)

Bioconductor-mirror/COHCAP documentation built on Aug. 6, 2017, 8:02 p.m.