R/data.R

In databio/GenomicDistributionsData: Reference data for GenomicDistributions package

#' hg19 chromosome sizes
#'
#' A dataset containing chromosome sizes for Homo sapiens hg19 genome assembly
#'
#' @format A named vectors of lengths with one item per chromosome
#' @source BSgenome.Hsapiens.UCSC.hg19 package
#' @name chromSizes_hg19
#' @docType data
#' @keywords datasets
#' @usage chromSizes_hg19(metadata=FALSE)
#' @param metadata \code{logical} value indicating whether only
#'     metadata should be returned or if the resource
#'     should be loaded
#' @return A vector of lengths
#' @examples 
#' hg19c = chromSizes_hg19()
#' 
NULL


#' hg38 chromosome sizes
#'
#' A dataset containing chromosome sizes for Homo sapiens hg38 genome assembly
#'
#' @format A named vectors of lengths with one item per chromosome
#' @source BSgenome.Hsapiens.UCSC.hg38 package
#' @name chromSizes_hg38
#' @docType data
#' @keywords datasets
#' @usage chromSizes_hg38(metadata=FALSE)
#' @param metadata \code{logical} value indicating whether only
#'     metadata should be returned or if the resource
#'     should be loaded
#' @return A vector of lengths
#' @examples 
#' hg38c = chromSizes_hg38()
#' 
NULL

#' mm9 chromosome sizes
#'
#' A dataset containing chromosome sizes for Mus musculus mm9 genome assembly
#'
#' @format A named vectors of lengths with one item per chromosome
#' @source BSgenome.MMusculus.UCSC.mm9 package
#' @name chromSizes_mm9
#' @docType data
#' @keywords datasets
#' @usage chromSizes_mm9(metadata=FALSE)
#' @param metadata \code{logical} value indicating whether only
#'     metadata should be returned or if the resource
#'     should be loaded
#' @return A vector of lengths
#' @examples 
#' mm9c = chromSizes_mm9()
#' 
NULL

#' mm10 chromosome sizes
#'
#' A dataset containing chromosome sizes for Mus musculus mm10 genome assembly
#'
#' @format A named vectors of lengths with one item per chromosome
#' @source BSgenome.MMusculus.UCSC.mm10 package
#' @name chromSizes_mm10
#' @docType data
#' @keywords datasets
#' @usage chromSizes_mm10(metadata=FALSE)
#' @param metadata \code{logical} value indicating whether only
#'     metadata should be returned or if the resource
#'     should be loaded
#' @return A vector of lengths
#' @examples 
#' mm10c = chromSizes_mm10() 
#' 
NULL


#' hg19 TSS locations
#'
#' A dataset containing Transcription Start Sites for Homo sapiens hg19 genome assembly
#'
#' @format A GRanges object with Transcription Start Site locations
#' @source EnsDb.Hsapiens.v75 package
#' @name TSS_hg19
#' @docType data
#' @keywords datasets
#' @usage TSS_hg19(metadata=FALSE)
#' @param metadata \code{logical} value indicating whether only
#'     metadata should be returned or if the resource
#'     should be loaded
#' @return A GRanges object with hg19 TSS locations.
#' @examples 
#' hg19TSS = TSS_hg19()
#' 
NULL

#' hg38 TSS locations
#'
#' A dataset containing Transcription Start Sites for the Homo sapiens 
#' hg38 genome assembly
#'
#' @format A GRanges object with Transcription Start Site locations
#' @source EnsDb.Hsapiens.v86 package
#' @name TSS_hg38
#' @docType data
#' @keywords datasets
#' @usage TSS_hg38(metadata=FALSE)
#' @param metadata \code{logical} value indicating whether only
#'     metadata should be returned or if the resource
#'     should be loaded
#' @return A GRanges object with hg38 TSS locations.
#' @examples 
#' hg38TSS = TSS_hg38()
#' 
NULL

#' mm10 TSS locations
#'
#' A dataset containing Transcription Start Sites for the Mus musculus 
#' mm10 genome assembly
#'
#' @format A named vectors of lengths with one item per chromosome
#' @source EnsDb.Mmusculus.v79 package
#' @name TSS_mm10
#' @docType data
#' @keywords datasets
#' @usage TSS_mm10(metadata=FALSE)
#' @param metadata \code{logical} value indicating whether only
#'     metadata should be returned or if the resource
#'     should be loaded
#' @return A GRanges object with mm10 TSS locations.
#' @examples 
#' mm10TSS = TSS_mm10()
#' 
NULL

#' mm9 TSS locations
#'
#' A dataset containing Transcription Start Sites for the Mus musculus 
#' mm9 genome assembly
#'
#' @format A named vectors of lengths with one item per chromosome
#' @source TxDb.Mmusculus.UCSC.mm9.knownGene package
#' @name TSS_mm9
#' @docType data
#' @keywords datasets
#' @usage TSS_mm9(metadata=FALSE)
#' @param metadata \code{logical} value indicating whether only
#'     metadata should be returned or if the resource
#'     should be loaded
#' @return A GRanges object with mm9 TSS locations.
#' @examples 
#' mm9TSS = TSS_mm9()
#' 
NULL


#' hg19 gene models
#'
#' A dataset containing gene models for Homo sapiens hg19 genome assembly
#'
#' @format A list of two GRanges objects, with genes and exons locations
#' @source EnsDb.Hsapiens.v75 package
#' @name geneModels_hg19
#' @docType data
#' @keywords datasets
#' @usage geneModels_hg19(metadata=FALSE)
#' @param metadata \code{logical} value indicating whether only
#'     metadata should be returned or if the resource
#'     should be loaded
#' @return A list with two GRanges objects.
#' @examples 
#' hg19GeneModels = geneModels_hg19()
#' 
NULL

#' hg38 gene models
#'
#' A dataset containing gene models for Homo sapiens hg38 genome assembly
#'
#' @format A list of two GRanges objects, with genes and exons locations
#' @source EnsDb.Hsapiens.v86 package
#' @name geneModels_hg38
#' @docType data
#' @keywords datasets
#' @usage geneModels_hg38(metadata=FALSE)
#' @param metadata \code{logical} value indicating whether only
#'     metadata should be returned or if the resource
#'     should be loaded
#' @return A list with two GRanges objects.
#' @examples 
#' hg38GeneModels = geneModels_hg38()
#' 
NULL

#' mm10 gene models
#'
#' A dataset containing gene models for Mus musculus mm10 genome assembly
#'
#' @format A list of two GRanges objects, with genes and exons locations
#' @source EnsDb.Mmusculus.v79 package
#' @name geneModels_mm10
#' @docType data
#' @keywords datasets
#' @usage geneModels_mm10(metadata=FALSE)
#' @param metadata \code{logical} value indicating whether only
#'     metadata should be returned or if the resource
#'     should be loaded
#' @return A list with two GRanges objects.
#' @examples 
#' mm10GeneModels = geneModels_mm10()
#' 
NULL

#' mm9 gene models
#'
#' A dataset containing gene models for Mus musculus mm9 genome assembly
#'
#' @format A list of two GRanges objects, with genes and exons locations
#' @source TxDb.Mmusculus.UCSC.mm9.knownGene package
#' @name geneModels_mm9
#' @docType data
#' @keywords datasets
#' @usage geneModels_mm9(metadata=FALSE)
#' @param metadata \code{logical} value indicating whether only
#'     metadata should be returned or if the resource
#'     should be loaded
#' @return A list with two GRanges objects.
#' @examples 
#' mm9GeneModels = geneModels_mm9()
#' 
NULL


#’ Cell type metadata matrix
#' 
#' Table the maps cell types to tissues and groups
#'
#' @format data.table with 3 columns (cellType, tissue and group) and 74 rows (one per cellType)
#' @source self-curated dataset
#' @name cellTypeMetadata
#' @docType data
#' @keywords datasets
NULL


#’ hg38 open signal matrix 
#' 
#' A dataset containing open chromatin regions across all cell types defined by ENCODE for Homo sapiens hg38
#'
#' Preparation steps:
#' \enumerate{
#'    \item{made a universe of regions by merging regions across cell types defined as opened in ENCODE}
#'    \item{took bigwig files from ENCODE for individual cell types, merged replicates, filtered out blacklisted sites}
#'    \item{evaluated the signal above regions defined by previous step}
#'    \item{performed quantile normalization}
#' }
#'
#' @format data.frame, rows represent whole selection of open 
#' chromatin regions across all cell types defined by ENCODE, columns are 
#' individual cell types and values are normalized open chromatin signal values.
#' @source \url{http://big.databio.org/open_chromatin_matrix/openSignalMatrix_hg38_percentile99_01_quantNormalized_round4d.txt.gz}
#' @name openSignalMatrix_hg38
#' @docType data
#' @keywords datasets
#' @usage openSignalMatrix_hg38(metadata=FALSE)
#' @param metadata \code{logical} value indicating whether only
#'     metadata should be returned or if the resource
#'     should be loaded
#' @return A data.frame with hg38 open chromatin regions.
#' @examples 
#' \dontrun{
#' hg38OpenSignal = openSignalMatrix_hg38()
#' }
#' 
NULL


#’ hg19 open signal matrix
#' 
#' A dataset containing open chromatin regions across all cell types defined by ENCODE for Homo Sapiens hg19
#' 
#' Preparation steps:
#' \enumerate{
#'    \item{made a universe of regions by merging regions across cell types defined as opened in ENCODE}
#'    \item{took bigwig files from ENCODE for individual cell types, merged replicates, filtered out blacklisted sites}
#'    \item{evaluated the signal above regions defined by previous step}
#'    \item{performed quantile normalization}
#' }
#'
#' @format data.frame, rows represent whole selection of open 
#' chromatin regions across all cell types defined by ENCODE, columns are 
#' individual cell types and values are normalized open chromatin signal values.
#' @source \url{http://big.databio.org/open_chromatin_matrix/openSignalMatrix_hg19_percentile99_01_quantNormalized_round4d.txt.gz}
#' @name openSignalMatrix_hg19
#' @docType data
#' @keywords datasets
#' @usage openSignalMatrix_hg19(metadata=FALSE)
#' @param metadata \code{logical} value indicating whether only
#'     metadata should be returned or if the resource
#'     should be loaded
#' @return A data.frame with hg19 open chromatin regions.
#' @examples 
#' \dontrun{
#' hg19OpenSignal = openSignalMatrix_hg19()
#' }
#' 
NULL


#’ mm10 open signal matrix
#' 
#' A dataset containing open chromatin regions across all cell types defined by ENCODE for Mus musculus mm10
#' 
#' Preparation steps:
#' \enumerate{
#'    \item{made a universe of regions by merging regions across cell types defined as opened in ENCODE}
#'    \item{took bigwig files from ENCODE for individual cell types, merged replicates, filtered out blacklisted sites}
#'    \item{evaluated the signal above regions defined by previous step}
#'    \item{performed quantile normalization}
#' }
#'
#' @format data.frame, rows represent whole selection of open 
#' chromatin regions across all cell types defined by ENCODE, columns are 
#' individual cell types and values are normalized open chromatin signal values.
#' @source \url{http://big.databio.org/open_chromatin_matrix/openSignalMatrix_mm10_percentile99_01_quantNormalized_round4d.txt.gz}
#' @name openSignalMatrix_mm10
#' @docType data
#' @keywords datasets
#' @usage openSignalMatrix_mm10(metadata=FALSE)
#' @param metadata \code{logical} value indicating whether only
#'     metadata should be returned or if the resource
#'     should be loaded
#' @return A data.frame with mm10 open chromatin regions.
#' @examples 
#' \dontrun{
#' mm10OpenSignal = openSignalMatrix_mm10()
#' }
#' 
NULL