To get the Beta values for the 65 SNP probes

getSnpBeta.R

# object must be an RGChannelSet object from the minfi package
getSnpBeta <- function(object){
    require(minfi)
  
    minfi:::.isRG(object)

    manifest <- getManifest(object)
    snpProbesII <- getProbeInfo(manifest, type = "SnpII")$Name

    M.II <- getGreen(object)[getProbeInfo(object, type = "SnpII")$AddressA,]
    U.II <- getRed(object)[getProbeInfo(object, type = "SnpII")$AddressA,]
    snpProbesI.Green <- getProbeInfo(manifest, type = "SnpI")[getProbeInfo(manifest, type = "SnpI")$Color=="Grn",]
    snpProbesI.Red <- getProbeInfo(manifest, type = "SnpI")[getProbeInfo(manifest, type = "SnpI")$Color=="Red",]

    M.I.Red <- getRed(object)[snpProbesI.Red $AddressB,]
    U.I.Red <- getRed(object)[snpProbesI.Red $AddressA,]
    M.I.Green <- getGreen(object)[snpProbesI.Green$AddressB,]
    U.I.Green <- getGreen(object)[snpProbesI.Green$AddressA,]

    M <- rbind(M.II, M.I.Red, M.I.Green)
    U <- rbind(U.II, U.I.Red, U.I.Green)

    rownames(M) <- rownames(U) <- c(snpProbesII, snpProbesI.Red$Name, snpProbesI.Green$Name)
    beta <- M/(U+M+100)
    return(beta)                               

}