BMplot: BMplot for Base Modification Visulization

#' Arabidopsis thaliana BSseq object created by DSS
#'
#' A data set contains methylation information
#' see data-row/A_thaliana_data_procession.R
"A_thaliana_BSobj"

#' Different methylation region created by DSS
#'
#' A data set contains information of different methylation region
#' see data-row/A_thaliana_data_procession.R
#' @format A data frame with 1 row and 9 variables
#' \describe{
#'   \item{chr}{chromosome, the chromosome information of dmR}
#'   \item{start}{the start site of dmR}
#'   \item{end}{the end site of dmR}
#'   \item{length}{the length of dmR}
#'   \item{nCG}{Number of CpG sites contained in the DMR}
#'   \item{meanMethy1}{Average methylation levels in two conditions}
#'   \item{meanMethy2}{Average methylation levels in two conditions}
#'   \item{diff.Methy}{The difference in the methylation levels between two conditions}
#'   \item{areaStat}{	The sum of the test statistics of all CpG sites within the DMR}
#' }
"A_thaliana_dmR"


#' Human BSseq object created by DSS
#'
#' A data set contains methylation information
#' see data-row/Human_data_procession.R
"Human_BSobj"

#' Different methylation region created by DSS
#'
#' A data set contains information of different methylation region
#' see data-row/Human_data_procession.R
#' @format A data frame with 29 row and 9 variables
#' \describe{
#'   \item{chr}{chromosome, the chromosome information of dmR}
#'   \item{start}{the start site of dmR}
#'   \item{end}{the end site of dmR}
#'   \item{length}{the length of dmR}
#'   \item{nCG}{Number of CpG sites contained in the DMR}
#'   \item{meanMethy1}{Average methylation levels in two conditions}
#'   \item{meanMethy2}{Average methylation levels in two conditions}
#'   \item{diff.Methy}{The difference in the methylation levels between two conditions}
#'   \item{areaStat}{	The sum of the test statistics of all CpG sites within the DMR}
#' }
"Human_dmR"


#' Simulated arabidopsis thaliana BSseq object created by DSS
#'
#' A simulated data set contains methylation information.
#' These data were created by finding the adenine positions in a specific region,
#' which was supposed to be the dmR, and assign the adenine sites with random values.
#' At last created BSseq object by DSS.
#' see data-row/simulated_A_thaliana_data_procession.R
"simulated_BSobj"

#' Different methylation region created by simulation
#'
#' A data set contains information of different methylation region
#' see data-row/simulated_A_thaliana_data_procession.R
#' @format A data frame with 1 row and 3 variables
#' \describe{
#'   \item{chr}{chromosome, the chromosome information of dmR}
#'   \item{start}{the start site of dmR}
#'   \item{end}{the end site of dmR}
#' }
"simulated_dmR"

#' Simulated IPD data of A_thaliana
#'
#' A data set contains simulated IPO information. This data set is simulated
#'    from GSE62206. We use two samples from GSE62206 and replace the previous value
#'    in GSE62206 with random IPO and IPO ratio.
#' see data-row/A_thaliana_IPO_data_procession.R
"simulated_IPD"