R/data.R

In biobenkj/compartmap: Higher-order chromatin domain inference in single samples from methylation arrays and single cells from scRNA-seq and scATAC-seq

#' Example scRNA-seq data for compartmap
#' 
#' This object was generated using the K562 data from the STORM-seq paper
#' and pre-processed using the scran and scater packages and TF-IDF
#' transformed.
#' 
#' @name k562_scrna_chr14
#' @docType data
#' @author Benjamin K Johnson \email{ben.johnson@vai.org}
#' @keywords data
#' @usage data(k562_scrna_chr14, package = "compartmap")
NULL

#' Example scRNA-seq data for compartmap
#' 
#' This object was generated using the K562 data from the STORM-seq paper
#' and pre-processed using the scran and scater packages and are raw counts.
#' 
#' @name k562_scrna_se_chr14
#' @docType data
#' @author Benjamin K Johnson \email{ben.johnson@vai.org}
#' @keywords data
#' @usage data(k562_scrna_raw, package = "compartmap")
NULL

#' Example scATAC-seq data for compartmap
#' 
#' This data was generated using the data from the reference via bwa mem
#' and pre-processing the data using the csaw package.
#' 
#' @name k562_scatac_chr14
#' @docType data
#' @author Benjamin K Johnson \email{ben.johnson@vai.org}
#' @references \url{https://www.ncbi.nlm.nih.gov//geo/query/acc.cgi?acc=GSE99172}
#' @keywords data
#' @usage data(k562_scatac_chr14, package = "compartmap")
NULL

#' Example SMART-seq3 scRNA-seq data for compartmap
#' 
#' This object was generated using the HEK293T data from the SMART-seq3 paper
#' 
#' @name ss3_umi_sce
#' @docType data
#' @author Benjamin K Johnson \email{ben.johnson@vai.org}
#' @references \url{https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-8735/}
#' @description Only keep chromosome 22 for the example
#' @keywords data
#' @usage data(ss3_umi_sce, package = "compartmap")
NULL

#' Example Illumina 450k methylation array data for compartmap
#' 
#' This data was generated using the data from the reference via the
#' sesamize function from the SeSAMe package.
#' 
#' @name array.data.chr14
#' @docType data
#' @author Benjamin K Johnson \email{ben.johnson@vai.org}
#' @references \url{https://f1000research.com/articles/5-1281/v3}
#' @keywords data
#' @usage data(meth_array_450k_chr14, package = "compartmap")
NULL

#' hg38 seqlengths as a GRanges object
#' 
#' This object was generated using the BSgenome.Hsapiens.UCSC.hg38 package.
#' The script used for this object is found in the inst/scripts directory
#' 
#' @name hg38.gr
#' @docType data
#' @author Benjamin K Johnson \email{ben.johnson@vai.org}
#' @keywords data
#' @usage data(hg38.gr, package = "compartmap")
NULL

#' hg19 seqlengths as a GRanges object
#' 
#' This object was generated using the Homo.sapiens package.
#' The script used for this object is found in the inst/scripts directory
#' 
#' @name hg19.gr
#' @docType data
#' @author Benjamin K Johnson \email{ben.johnson@vai.org}
#' @keywords data
#' @usage data(hg19.gr, package = "compartmap")
NULL

#' mm10 seqlengths as a GRanges object
#' 
#' This object was generated using the Mus.musculus package.
#' The script used for this object is found in the inst/scripts directory
#' 
#' @name mm10.gr
#' @docType data
#' @author Benjamin K Johnson \email{ben.johnson@vai.org}
#' @keywords data
#' @usage data(mm10.gr, package = "compartmap")
NULL

#' mm9 seqlengths as a GRanges object
#' 
#' This object was generated using the BSgenome.Mmusculus.UCSC.mm9 package.
#' The script used for this object is found in the inst/scripts directory
#' 
#' @name mm9.gr
#' @docType data
#' @author Benjamin K Johnson \email{ben.johnson@vai.org}
#' @keywords data
#' @usage data(mm9.gr, package = "compartmap")
NULL

#' hg38 open sea CpG as a GRanges object
#' 
#' This object was generated using the BSgenome.Hsapiens.UCSC.hg38 package.
#' 
#' @name openSeas.hg38
#' @docType data
#' @author Benjamin K Johnson \email{ben.johnson@vai.org}
#' @keywords data
#' @usage data(openSeas.hg38, package = "compartmap")
NULL

#' hg19 open sea CpG as a GRanges object
#' 
#' This object was generated using the Homo.sapiens package.
#' 
#' @name openSeas.hg19
#' @docType data
#' @author Benjamin K Johnson \email{ben.johnson@vai.org}
#' @keywords data
#' @usage data(openSeas.hg19, package = "compartmap")
NULL

#' mm10 open sea CpG as a GRanges object
#' 
#' This object was generated using the Mus.musculus package.
#' 
#' @name openSeas.mm10
#' @docType data
#' @author Benjamin K Johnson \email{ben.johnson@vai.org}
#' @keywords data
#' @usage data(openSeas.mm10, package = "compartmap")
NULL

#' mm9 open sea CpG as a GRanges object
#' 
#' This object was generated using the BSgenome.Mmusculus.UCSC.mm9 package.
#' 
#' @name openSeas.mm9
#' @docType data
#' @author Benjamin K Johnson \email{ben.johnson@vai.org}
#' @keywords data
#' @usage data(openSeas.mm9, package = "compartmap")
NULL