getAdj: Extract values adjusted for unwanted variation by RUVm

In Oshlack/missMethyl: Analysing Illumina HumanMethylation BeadChip Data

Extract values adjusted for unwanted variation by RUVm

Description

Extract values adjusted for unwanted variation by RUVm.

Usage

getAdj(Y, fit)

Arguments

Y	A matrix of M-values.
fit	The list list object produced by RUVfit.

Details

This function extracts values adjusted for unwanted variation by RUVm. These values are ONLY intendeded to be used for visualisation purposes. It is NOT recommended that they are used for any further analysis.

Value

An matrix of M-values.

Author(s)

Jovana Maksimovic

See Also

MArrayLM

Examples

if(require(minfi) & require(minfiData) & require(limma)) {

# Get methylation data for a 2 group comparison
meth <- getMeth(MsetEx)
unmeth <- getUnmeth(MsetEx)
Mval <- log2((meth + 100)/(unmeth + 100))

group <- factor(pData(MsetEx)$Sample_Group, labels=c(0,1))
design <- model.matrix(~group)

# Perform initial analysis to empirically identify negative control features 
# when not known a priori
lFit <- lmFit(Mval,design)
lFit2 <- eBayes(lFit)
lTop <- topTable(lFit2,coef=2,num=Inf)

# The negative control features should *not* be associated with factor of 
# interest but *should* be affected by unwanted variation 
ctl <- rownames(Mval) %in% rownames(lTop[lTop$adj.P.Val > 0.5,])

# Perform RUV adjustment and fit
fit <- RUVfit(Y=Mval, X=group, ctl=ctl)
fit2 <- RUVadj(Y=Mval, fit=fit)

# get adjusted values
Madj <- getAdj(Y=Mval,fit=fit)
}

Oshlack/missMethyl documentation built on March 26, 2023, 1:50 p.m.