getAdj {missMethyl} | R Documentation |
Extract values adjusted for unwanted variation by RUVm.
getAdj(Y, fit)
Y |
A matrix of M-values. |
fit |
The list |
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.
An matrix of M-values.
Jovana Maksimovic
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) }