COHCAP (version 1.10.0)

COHCAP.avg.by.site: CpG Island Differential Methylation Analysis (Average by Site Workflow).

Description

Provides statistics for CpG islands as well as a list of differentially methylated sites. CpG Island statistics are calculated by averaging beta values among samples per site and comparing the average beta values across groups (considering the pairing between sites).

List of differentially methylated islands will be created in the "CpG_Island" folder. Table of statistics for all CpG islands will be created in the "Raw_Data" folder.

Usage

COHCAP.avg.by.site(site.table, project.name, project.folder,
				methyl.cutoff=0.7, unmethyl.cutoff = 0.3,
				delta.beta.cutoff = 0.2, pvalue.cutoff=0.05,
				fdr.cutoff=0.05, num.groups=2, num.sites=4,
				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

methyl.cutoff

Minimum beta or percentage methylation value to be used to define a methylated CpG site. Default is 0.7 (used for beta values), which would correspond to 70 Used for either 1-group or 2-group comparison.

unmethyl.cutoff

Minimum beta or percentage methylation value to be used to define an unmethylated CpG site. Default is 0.3 (used for beta values), which would correspond to 30 Used for either 1-group or 2-group comparison.

delta.beta.cutoff

The minimum absolute value for delta-beta values (mean treatment beta - mean reference beta) to define a differentially methylated CpG site. Only used for 2-group comparison.

pvalue.cutoff

Maximum p-value allowed to define a CpG island as differentially methylated.

fdr.cutoff

Maximum False Discovery Rate (FDR) allowed to define CpG island as differentially methylated.

num.groups

Number of groups described in sample description file. COHCAP algorithm differs when analysing 1-group, 2-group, or >2-group comparisons. COHCAP cannot currently analyze continuous phenotypes.

num.sites

Minimum number of differentially methylated sites to define a differentially methylated CpG island.

output.format

Format for output tables: 'xls' for Excel file, 'txt' for tab-delimited text file

Value

Data frame of average beta (or percentage methylation) statistics and/or p-value / false discovery rate statistics (per CpG island).The content of the data frame depends upon the number of groups specified for analysis. All workflows provide p-values and FDR values. 1 and 2 group comparisons provide counts for methylated and unmethylated sites as well as an overall methylation status per island. >2 group comparisons only provide counts for the total number of differentially methylated sites.This data frame can be used for integration analysis.

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 <- getwd()
project.name <- "450k_avg_by_site_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")
filtered.islands <- COHCAP.avg.by.site(filtered.sites, project.name,
				project.folder)