assocComp-methods: Associate principal components with sample annotations

In al2na/methylKit: DNA methylation analysis from high-throughput bisulfite sequencing results

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)

al2na/methylKit documentation built on Feb. 1, 2024, 4:42 p.m.