R/CreateOutputDF.R

In lissettegomez/coMethDMR: Accurate identification of co-methylated and differentially methylated regions in epigenome-wide association studies

#' Create Output Dataframe
#'
#' @param keepCpGs_df a data frame with CpG = CpG name,
#'    keep = indicator for co-methylated CpG,
#'    r_drop = correlation between the CpG with rest of the CpGs
#' @param keepContiguousCpGs_df a data frame with ProbeID = CpG name,
#'    Subregion = contiguous comethylated subregion number
#' @param CpGsOrdered_df a data frame of CpG location with
#'    chr = chromosome number, pos = genomic position, cpg = CpG name
#' @param returnAllCpGs indicates if outputting all the CpGs in the region
#'    when there is not a contiguous comethylated region or
#'    only the CpGs in the contiguous comethylated regions
#'
#' @return a data frame with CpG = CpG name,
#'    Chr = chromosome number,
#'    MAPINFO = genomic position,
#'    r_drop = correlation between the CpG with rest of the CpGs,
#'    keep = indicator for co-methylated CpG,
#'    keep_contiguous = contiguous comethylated subregion number
#'
#' @keywords internal
#'
#' @export
#'
#' @examples
#'    data(betasChr22_df)
#'    CpGsChr22_char<-c("cg02953382", "cg12419862", "cg24565820", "cg04234412",
#'       "cg04824771", "cg09033563", "cg10150615", "cg18538332", "cg20007245",
#'       "cg23131131", "cg25703541")
#'    CpGsOrdered_df <- OrderCpGsByLocation(
#'       CpGsChr22_char, arrayType="450k", output = "dataframe"
#'    )
#'    betaCluster_mat <- betasChr22_df[CpGsOrdered_df$cpg,]
#'    betaClusterTransp_mat <- t(betaCluster_mat)
#'    keepCpGs_df <- MarkComethylatedCpGs(betaCluster_mat = betaClusterTransp_mat)
#'    keepContiguousCpGs_df <- FindComethylatedRegions(CpGs_df = keepCpGs_df)
#'    CreateOutputDF(keepCpGs_df, keepContiguousCpGs_df, CpGsOrdered_df)
CreateOutputDF <- function(keepCpGs_df,
                           keepContiguousCpGs_df,
                           CpGsOrdered_df,
                           returnAllCpGs = FALSE){

  if (returnAllCpGs == FALSE & all(keepContiguousCpGs_df$Subregion == 0)){

    NULL

  } else {

    output_df <- merge(
      keepCpGs_df, keepContiguousCpGs_df, by.x = "CpG", by.y = "ProbeID", all.x = TRUE
    )
    output2_df <- merge(
      CpGsOrdered_df, output_df, by.x = "cpg", by.y = "CpG"
    )

    output3_df <- output2_df[order(output2_df$chr, output2_df$pos), ]
    output3_df [is.na(output3_df)] <- 0

    coMethCpGs_df <- data.frame(
      Region = NameRegion(CpGsOrdered_df),
      CpG = output3_df$cpg,
      Chr = output3_df$chr,
      MAPINFO = output3_df$pos,
      r_drop = output3_df$r_drop,
      keep = output3_df$keep,
      keep_contiguous = output3_df$Subregion
    )

    coMethCpGs_df


  }

}