COHCAP.qc {COHCAP} | R Documentation

## DNA Methylation Quality Control Statistics

### Description

Provides descriptive statistics (median, top/bottom quartiles, mininum,maximum), sample histograms, sample dendrogram, principal component analysis plot.

Output files will be created in the "QC" subfolder.

### Usage

    COHCAP.qc(sample.file, beta.table, project.name, project.folder,
    				plot.legend=TRUE, color.palette = c("red","blue",
    				"green","orange","purple","cyan","pink","maroon",
    				"yellow","grey","black",colors()))

### 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
`plot.legend` | A logical value: Should legend be plotted within QC figures?
`color.palette` | Colors for primary variable (specified in the second column of the sample file). Remember, COHCAP can only analyze discrete variables categoried with groups (preferably with replicates).

### 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")
    COHCAP.qc(sample.file, beta.table, project.name, project.folder)

[Package COHCAP version 1.36.0 Index]