R/getAnnot.R

In methylGSA: Gene Set Analysis Using the Outcome of Differential Methylation

#' @title Get CpG annotation
#'
#' @description This function gets CpG IDs and their corresponding gene symbols.
#' @param array.type A string. Either "450K" or "EPIC". Default is "450K".
#' @param group A string. "all", "body", "promoter1" or "promoter2". 
#' Default is "all". If group = "body", only CpGs on gene body will be 
#' pulled out. If group = "promoter1" or group = "promoter2", 
#' only CpGs on promoters will be pulled out. Here is the definition of "body", 
#' "promoter1" and "promoter2" according to the annotation in 
#' IlluminaHumanMethylation450kanno.ilmn12.hg19 or 
#' IlluminaHumanMethylationEPICanno.ilm10b4.hg19. 
#' \itemize{
#'   \item body: CpGs whose gene group correspond to "Body" or "1stExon" 
#'   \item promoter1: CpGs whose gene group correspond to "TSS1500" or "TSS200"
#'   \item promoter2: CpGs whose gene group correspond to "TSS1500", "TSS200", 
#'   "1stExon", or "5'UTR". 
#' }
#' If group = "all", all CpGs will be pulled out.
#' @import IlluminaHumanMethylation450kanno.ilmn12.hg19
#' @import IlluminaHumanMethylationEPICanno.ilm10b4.hg19
#' @importFrom stringr str_length
#' @details The implementation of the function is modified
#' from .flattenAnn function in missMethyl package.
#' @return A data frame contains CpG IDs and gene symbols.
#' @references Hansen KD (2016). IlluminaHumanMethylation450kanno.ilmn12.hg19:
#' Annotation for Illumina's 450k methylation arrays. R package version 0.6.0.
#' @references Hansen KD (2017). IlluminaHumanMethylationEPICanno.ilm10b4.hg19:
#' Annotation for Illumina's EPIC methylation arrays. R package version 0.6.0,
#' https://bitbucket.com/kasperdanielhansen/Illumina_EPIC.
#' @references Phipson B, Maksimovic J and Oshlack A (2015).
#' “missMethyl: an R package for analysing methylation data from
#' Illuminas HumanMethylation450 platform.” Bioinformatics, pp. btv560.

getAnnot = function(array.type, group = "all"){
    if(array.type=="450K"){
        FullAnnot = tryCatch({
            getAnnotation(IlluminaHumanMethylation450kanno.ilmn12.hg19)
            },
            error = function(e){
                stop("IlluminaHumanMethylation450kanno.ilmn12.hg19 needs to
be installed and loaded before running methylglm/methylRRA")
            })
    }else{
        FullAnnot = tryCatch({
            getAnnotation(IlluminaHumanMethylationEPICanno.ilm10b4.hg19)
        },
        error = function(e){
            stop("IlluminaHumanMethylationEPICanno.ilm10b4.hg19 needs to
be installed and loaded before running methylglm/methylRRA")
        })
    }
        
    FullAnnot = FullAnnot[,c("Name","UCSC_RefGene_Name","UCSC_RefGene_Group")]
    FullAnnot = FullAnnot[str_length(rownames(FullAnnot))==10,]
    FullAnnot = FullAnnot[!FullAnnot$UCSC_RefGene_Name=="",]
    ## get the first gene in each USCS_RefGene_Name
    temp = vapply(strsplit(FullAnnot$UCSC_RefGene_Name,split=";"),
                        '[', 1, FUN.VALUE=character(1))
    FullAnnot$UCSC_RefGene_Name = temp
    ## get the first gene group in each UCSC_RefGene_Group
    temp = vapply(strsplit(FullAnnot$UCSC_RefGene_Group,split=";"),
        '[', 1, FUN.VALUE=character(1))
    FullAnnot$UCSC_RefGene_Group = temp
    
    if(group == "body"){
        FullAnnot = 
            FullAnnot[FullAnnot$UCSC_RefGene_Group%in%c("Body", "1stExon"),]
    }
        
    if(group == "promoter1"){
        FullAnnot = FullAnnot[grepl("TSS",FullAnnot$UCSC_RefGene_Group),]
    }
    
    if(group == "promoter2"){
        FullAnnot = 
            FullAnnot[FullAnnot$UCSC_RefGene_Group%in%c("TSS200", "TSS1500", 
                "1stExon", "5'UTR"),]
    }
        
    return(FullAnnot)
}