assocComp-methods: Associate principal components with sample annotations

Description Usage Arguments Value Author(s) Examples

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

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  assocComp(mBase, sampleAnnotation)

Arguments

mBase

methylBase 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'), (named 'vars') and a p-value matrix showing association p-values between sample annotations and principal components (named 'association').

Author(s)

Altuna Akalin

Examples

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

vd4mmind/methylkit documentation built on May 3, 2019, 4:57 p.m.