To remove sex chromosome probes from a 450k matrix

makeAutosomal.R

makeAutosomal <- function(matrix){
    require(IlluminaHumanMethylation450kanno.ilmn12.hg19)
    ann <- getAnnotation(IlluminaHumanMethylation450kanno.ilmn12.hg19)
    good.probes <- rownames(ann)[-which(ann$chr=="chrX" | ann$chr=="chrY")]
    matrix[rownames(matrix) %in% good.probes,]
}


makeX <- function(matrix){
    require(IlluminaHumanMethylation450kanno.ilmn12.hg19)
    ann <- getAnnotation(IlluminaHumanMethylation450kanno.ilmn12.hg19)
    good.probes <- rownames(ann)[ann$chr=="chrX"]
    matrix[rownames(matrix) %in% good.probes,]
}


makeY <- function(matrix){
    require(IlluminaHumanMethylation450kanno.ilmn12.hg19)
    ann <- getAnnotation(IlluminaHumanMethylation450kanno.ilmn12.hg19)
    good.probes <- rownames(ann)[ann$chr=="chrY"]
    matrix[rownames(matrix) %in% good.probes,]
}