R/data.R

In CellFateNucOrg/nanodsmf: Analyse nanopore dual enzyme single molecule footprinting data (nanoDSMF)

#' Example of calling CpG methylation on GpC methylated amplicon
#'
#' a PCR amplicon of ttTi5605 was GpC methylated in vitro
#' with MCviPI enzyme and then CpG methylation was called on
#' the data using nanopolish v0.11.0
#'#'
#' @docType data
#' @usage data(MCviPI_CpG)
#' @format An object of type data.frame
#' @source 20171027_Minion_TMP_Meth
"MCviPI_CpG"

#' Example of calling GpC methylation on GpC methylated amplicon
#'
#' a PCR amplicon of ttTi5605 was GpC methylated in vitro
#' with MCviPI enzyme and then GpC methylation was called on
#' the data using nanopolish v0.11.0
#'
#' @docType data
#' @usage data(MCviPI_GpC)
#' @format An object of type data.frame
#' @source 20171027_Minion_TMP_Meth
"MCviPI_GpC"

#' Example of calling CpG methylation on CpG methylated amplicon
#'
#' a PCR amplicon of ttTi5605 was CpG methylated in vitro
#' with MSssI enzyme and then CpG methylation was called on
#' the data using nanopolish v0.11.0
#'
#' @docType data
#' @usage data(MSssI_CpG)
#' @format An object of type data.frame
#' @source 20171027_Minion_TMP_Meth
"MSssI_CpG"

#' Example of calling GpC methylation on CpG methylated amplicon
#'
#' a PCR amplicon of ttTi5605 was CpG methylated in vitro
#' with MSssI enzyme and then GpC methylation was called on
#' the data using nanopolish v0.11.0
#'
#' @docType data
#' @usage data(MSssI_GpC)
#' @format An object of type data.frame
#' @source 20171027_Minion_TMP_Meth
"MSssI_GpC"





#' Example of calling CpG methylation on GpC methylated amplicon
#'
#' a PCR amplicon of ttTi5605 was GpC methylated in vitro
#' with MCviPI enzyme and then CpG methylation was called on
#' the data using nanopolish v0.11.0 to call freq of methylation per site.
#'#'
#' @docType data
#' @usage data(MCviPI_freqCmG)
#' @format An object of type data.frame
#' @source 20171027_Minion_TMP_Meth
"MCviPI_freqCmG"

#' Example of calling GpC methylation on GpC methylated amplicon
#'
#' a PCR amplicon of ttTi5605 was GpC methylated in vitro
#' with MCviPI enzyme and then GpC methylation was called on
#' the data using nanopolish v0.11.0 to call freq of methylation per site.
#'
#' @docType data
#' @usage data(MCviPI_freqGCm)
#' @format An object of type data.frame
#' @source 20171027_Minion_TMP_Meth
"MCviPI_freqGCm"

#' Example of calling CpG methylation on CpG methylated amplicon
#'
#' a PCR amplicon of ttTi5605 was CpG methylated in vitro
#' with MSssI enzyme and then CpG methylation was called on
#' the data using nanopolish v0.11.0 to call freq of methylation per site.
#'
#' @docType data
#' @usage data(MSssI_freqCmG)
#' @format An object of type data.frame
#' @source 20171027_Minion_TMP_Meth
"MSssI_freqCmG"

#' Example of calling GpC methylation on CpG methylated amplicon
#'
#' a PCR amplicon of ttTi5605 was CpG methylated in vitro
#' with MSssI enzyme and then GpC methylation was called on
#' the data using nanopolish v0.11.0 to call freq of methylation per site.
#'
#' @docType data
#' @usage data(MSssI_freqGCm)
#' @format An object of type data.frame
#' @source 20171027_Minion_TMP_Meth
"MSssI_freqGCm"





#' DNAstringset for sequence used in example data
#'
#' DNAstringset object with fasta sequence of genome
#'
#' @docType data
#' @usage data(ttTi5605dna)
#' @format An object of type DNAStringset
"ttTi5605dna"


#' GenomicRanges for sequence used in example data
#'
#' GRanges or GRangesList type object for genome
#'
#' @docType data
#' @usage data(ttTi5605gr)
#' @format An object of type GRanges
"ttTi5605gr"