minfi betas and residuals from methylation models

In the HELIX project we decided to use residuals instead of M values for the methylation analyses. So, how we get the residuals of a basic lineal model?

Libraries and Data

First of all we load the libraries we will use in this test:

library( limma )    # We use lmFit to fit the lineal model
library( minfi )    # Methylation data is saved as a GenomicRatioSet
library( SmartSVA ) # We want to compute the SVA to correct methylation data
library( isva )     # "
library( Biobase )  # We will sabe the residuals in an ExpressionSet

Once the libraries are loaded we proceed to obtain the methylation data:

load( "/.../methylation/FinalData/methylome_v3.Rdata" )

The loaded object looks like:

> methylome
class: GenomicRatioSet 
dim: 386518 1192 
assays(2): Beta CN
rownames(386518): cg13869341 cg24669183 ... cg22662321 cg09226288
rowData names(14): Forward_Sequence SourceSeq ...
  Regulatory_Feature_Group DHS
colnames(1192): BIB_15586_1X BIB_33043_1X ... KAN_257_1X SAB_430_1X
colData names(39): HelixID SampleID ... Slide Basename
  array: IlluminaHumanMethylation450k
  annotation: ilmn12.hg19
  Method: NA
  minfi version: NA
  Manifest version: NA

Next step is to obtain the M values of the methylation. To this we should use the method getM from minfi. Unfortunately, getM uses the getBeta from minfi that has some type of bug.

Obtaine M values

So, before any other step, we implement a new function to get the betas and a new function to get the Ms:

getBeta2 <- function( ms, offset ) {
  bs <- getBeta( ms )
  bs[ bs == 0 ] <- offset
  bs[ bs == 1 ] <- 1 - offset

getM2 <- function( ms, offset = 0.001 ) {
    bs <- getBeta2( methylome_subcohort, offset )
    ms <- logit2( bs )

And we obtain the M values of our GenomicRatioSet:

m <- getM2( methylome )

Applying SVA (SmartSVA)

To apply SVA and obtain the corresponding surrogate variables to correct of undesired effects the methylation data we need to obtain the phenotype data or the column data.

pd <- colData( methylome )

Then we apply the SmartSVA pipeline using the basic model ( model adjusted by cohort, sex and age):

Y.r <- t( resid( lm( t( m ) ~ cohort + sex + age_years, data = pd ) ) )
n.sv <- EstDimRMT( Y.r, FALSE )$dim + 1
mod <- model.matrix( ~ cohort + sex + age_years, pd )
sv.obj <- smartsva.cpp( m, mod, mod0 = NULL, n.sv = n.sv )

The content of sv.obj corresponds to the surrogate variables created to correct the undesired effects in the methylation data. So, the next step is to create a model including this surrogate variables and finally obtain the residuals of the basic-surrogate model.

The new model is easily created using cbind:

model <- cbind( mod, sv.obj$sv)

Finally we get the residuals of the new model with:

res <- residuals( lmFit( m, model ), m )

Encapsulate the residuals in an ExposomeSet

So, to save the residuals and be able to use them in limma-like pipelines we encapsulate them in an ExposomeSet. So, first we get the phenotype data and feature data.

fd <- as.data.frame( cbind( 
    as.data.frame( rowRanges( methylome_subcohort ) ),
    rowData( methylome_subcohort )
) )

pd <- as.data.frame( colData( methylome_subcohort ) )

And second we encapsulate the residuals and the two data-sets in a new ExposomeSet:

methylome_residuals <- ExpressionSet(
    assayData = res,
    phenoData = AnnotatedDataFrame( pd ),
    featureData = AnnotatedDataFrame( fd )

The created ExposomeSet looks like:

> methylome_residuals_subcohort
ExpressionSet (storageMode: lockedEnvironment)
assayData: 386518 features, 1192 samples
  element names: exprs
protocolData: none
  sampleNames: BIB_15586_1X BIB_33043_1X ... SAB_430_1X (1192 total)
  varLabels: HelixID SampleID ... Basename (39 total)
  varMetadata: labelDescription
  featureNames: cg13869341 cg24669183 ... cg09226288 (386518 total)
  fvarLabels: seqnames start ... DHS.1 (33 total)
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'