assocComp {methylKit} | R Documentation

## Associate principal components with sample annotations

### Description

This function associates principal components with sample annotations such as age, gender, batch_id. Can be used to detect which batch effects are associated with the variation in the methylation values.

### Usage

    assocComp(mBase, sampleAnnotation)

### Arguments

`mBase` | `methylBase` or `methylBaseDB` object with no NA values in the data part.
`sampleAnnotation` | a data frame where columns are different annotations and rows are the samples, in the same order as in the methylBase object.

### Value

a named list of principal component matrix (named 'pcs'), by principal compopents (named 'vars') and a p-value matrix showing association p-values between sample annotations and principal components (named 'association').

### Author(s)

Altuna Akalin

### Examples

    data(methylKit)
    sampleAnnotation=data.frame(batch_id=c("a","a","b","b"),age=c(19,34,23,40))
    as=assocComp(mBase=methylBase.obj,sampleAnnotation)

[Package methylKit version 1.16.1 Index]