COHCAP.denovo {COHCAP} | R Documentation |
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.
COHCAP.denovo(site.table, project.name, project.folder, min.sites = 4, max.dist = 500, output.format = "xls")
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. |
Returns a table of clusters of differentially methylated sites, defined using criteria specified to COHCAP.site()
COHCAP Discussion Group: http://sourceforge.net/p/cohcap/discussion/general/
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)