COHCAP (version 1.10.0)

COHCAP.site: CpG Site Differential Methylation Analysis

Description

Provides statistics for CpG sites as well as a list of differentially methylated sites. Can also provide .wig files for visualization in IGV, UCSC Genome Browser, etc.

List of differentially methylated sites and .wig files will be created in the "CpG_Site" folder. Table of statistics for all CpG sites will be created in the "Raw_Data" folder.

Usage

COHCAP.site(sample.file, beta.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, ref="none", num.groups=2,
				create.wig = TRUE, paired=FALSE, output.format = "xls")

Arguments

sample.file

Tab-delimited text file providing group attributions for all samples considered for analysis.

beta.table

Data frame with CpG sites in columns (with DNA methylation represented as beta values or percentage methylation), samples in columns, and CpG site annotations are included (in columns 2-5). The COHCAP.annotate 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 site as differentially methylated. Used only for comparisons with at least 2 groups (with 3 replicates per group)

fdr.cutoff

Maximum False Discovery Rate (FDR) allowed to define a site as differentially methylated. Used only for comparisons with at least 2 groups (with 3 replicates per group)

ref

Reference group used to define baseline methylation levels. Only used for 2-group comparison

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.

create.wig

A logical value: Create .wig files (using average beta and delta-beta values)? In the standalone version of COHCAP, this was only an option when using the "Average by Site" workflow (because that was the only situation where the analysis method matched the visualization). .wig files are defined with respect to hg19 (for pre-defined annotation files) and can be visualized using IGV, UCSC Genome Browser, etc.

paired

A logical value: Is there any special pairing between samples in different groups? If so, the pairing variable must be specified in the 3rd column of the sample description file. Used for p-value calculation, so this only applies to comparisons with at least 2 groups.

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.The content of the data frame depends upon the number of groups specified for analysis (avg.beta only for 1-group; avg.beta, delta.beta, p-value, and FDR for 2-group; p-value and FDR only for >2 groups).This data frame is used for CpG island 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_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")