R/chic.data.R
In carmencita/ChIC.data: ChIC package data
#' Histone mark compendium
#'
#' Histone mark ChIP-seq compendium for the ChIC package.
#' The compendium contains quality control metrics and metadata for 2204
#' histone mark samples
#' analysed from ENCODE and Roadmap Epigenomics.
#'
#' @docType data
#'
#' @keywords histone marks
#' @keywords quality control metrics
#' @keywords compendium
#'
#' @usage data(compendium_db)
#'
#' @format Data frame with 251 variables (quality control metrics, metadata)
#' for each analysed sample.
#'
#' @source XX
#'
"compendium_db"
#' Transcription factor compendium
#'
#' Transcription factor ChIP-seq compendium for the ChIC package.
#' The compendium contains quality control metrics and metadata for 1350
#' transcription factors analysed from ENCODE.
#'
#'
#' @docType data
#'
#' @keywords tf
#' @keywords quality control metrics
#' @keywords compendium
#'
#' @usage data(compendium_db_tf)
#'
#' @format Data frame with 251 variables (quality control metrics, metadata)
#' for each analysed sample.
#'
#' @source XX
#'
"compendium_db_tf"
#' List with definitions
#'
#' List containing information about chromatin marks, transcription
#' factors, definitions for broad and sharp class.
#'
#' @docType data
#'
#' @keywords definitions
#'
#' @usage data(classesDefList)
#' @import caret
#' @format A list of 5, containing a vector with chromatin mark names,
#' TF names, the members of sharp binding marks, broad binding marks
#' and RNApol2
#'
#' \itemize{
#' \item Hlist: vector with chromatin marks
#' \item allSharp: vector with sharp binding marks
#' \item allBroad: vector with broad binding marks
#' \item RNAPol2 : RNApol2
#' \item TF: vector with TF names
#'}
#'
"classesDefList"
#' Random forest models for chromatin marks ChIP-seq
#' experiment classification
#'
#' Random forest models based on ENCODE and Roadmap data for ChIP-seq
#' experiment classification using the ChIC package.
#'
#' @docType data
#'
#' @keywords classification
#'
#' @usage data(rf_models)
#' @import caret
#' @import randomForest
#' @format A list of 7 random forest models for the different
#' chromatin marks and transcription factors:
#'
#' \itemize{
#' \item Broad : model for broad binding marks
#' \item H3K9me3 : model for H3K9me3
#' \item H3K27me3 : model for H3K27me3
#' \item H3K36me3 : model for H3K36me3
#' \item RNAPol2 : model for RNAPol2
#' \item Sharp : model for sharp binding marks
#' \item TF : model for transcription factors
#'}
#'
"rf_models"
#' Example results from the qualityScores_EM() function based on the example ChIP-seq data for the Vignette for ChIC package
#'
#' Example data to be used in the vignette for ChIC package
#'
#' @docType data
#'
#' @keywords EM_Results
#'
#' @usage data(EM_Results)
#' @format list containing EM scores and filtered reads
#'
#'
"EM_Results"
#' ChIP-seq bam file stored as spp tag-list for
#' a subset of chromosomes for the chip
#'
#' Example data for manual and vignette.
#' tag-list created with the
#' read.bam.tags() function from spp package.
#' The original bam file has been dowloaded from ENCODE
#' (ID: ENCFF000BFX).
#'
#' @docType data
#'
#' @keywords bamfile
#'
#' @usage data(chipSubset)
#' @format list of 2 elements containing the reads and the
#' read quality of the ChIP.
#'
#' \itemize{
#' \item tags : list containing the start coordinates
#' of each read aligned (ChIP) (3'end)
#' \item quality: list containing the read quality
#' of each read
#'}
#'
"chipSubset"
#' ChIP-seq bam file stored as spp tag-list for
#' a subset of chromosomes for the input
#'
#' Example data for manual and vignette.
#' Tag-list created with the
#' read.bam.tags() function from spp package for
#' the input data.
#' The original bam file has been dowloaded from ENCODE
#' (ID: ENCFF000BDQ).
#'
#' @docType data
#'
#' @keywords bamfile
#'
#' @usage data(inputSubset)
#' @format list of 2 elements containing the reads and the
#' read quality of the input.
#'
#' \itemize{
#' \item tags : list containing the start coordinates
#' of each read aligned (input) (3'end)
#' \item quality: list containing the read quality
#' of each read
#'}
#'
"inputSubset"
##profile compendiums
#' Metagene profile data for chromatin marks
#'
#' Compendium of averaged metagene profiles for the ChIC package. Contains
#' averaged metagene profiles for following ChIP-seq datasets from ENCODE
#' and Roadmap Epigenomics.
#'
#' \itemize{
#' \item H2A.Z
#' \item H2AFZ
#' \item H2AK5ac
#' \item H2AK9ac
#' \item H2BK120ac
#' \item H2BK12ac
#' \item H2BK15ac
#' \item H2BK20ac
#' \item H2BK5ac
#' \item H3K14ac
#' \item H3K18ac
#' \item H3K23ac
#' \item H3K23me2
#' \item H3K27ac
#' \item H3K27me3
#' \item H3K36me3
#' \item H3K4ac
#' \item H3K4me1
#' \item H3K4me2
#' \item H3K4me3
#' \item H3K56ac
#' \item H3K79me1
#' \item H3K79me2
#' \item H3K9ac
#' \item H3K9me1
#' \item H3K9me3
#' \item H3T11ph
#' \item H4K12ac
#' \item H4K20me1
#' \item H4K5ac
#' \item H4K8ac
#' \item H4K91ac
#' \item POLR2A
#' \item POLR2AphosphoS2
#' \item POLR2AphosphoS5
#' }
#'
#' @docType data
#'
#' @keywords metagene profiles
#' @keywords compendium
#' @keywords chromatin marks
#'
#' @usage data(compendium_profiles)
#'
#' @format A list of data frames with the coordinates of the
#' metagene profile of the respective chromatin mark.
#'
#' x : genomic coordinates
#' mean : the mean of the signal intensity in the compendium
#' sd : the standard deviation of the signal intensity in the
#' compendium
#' q1..q5 : being the respective quantile of the value distribution
#' sderr : standard error
#' setSize : setsize analysed
#' @source XX
#'
"compendium_profiles"
#' Metagene profile data for transcription factors
#'
#' Compendium of averaged metagene profiles for the ChIC package. Contains
#' averaged metagene profiles for following ChIP-seq datasets from ENCODE.
#'
#' \itemize{
#' \item ARID3A
#' \item ATF2
#' \item ATF3
#' \item BACH1
#' \item BATF
#' \item BCL11A
#' \item BCL3
#' \item BCLAF1
#' \item BHLHE40
#' \item BRCA1
#' \item CBX2
#' \item CBX3
#' \item CEBPB
#' \item CEBPD
#' \item CEBPZ
#' \item CHD1
#' \item CHD2
#' \item CHD4
#' \item CREB1
#' \item CREBBP
#' \item CTCF
#' \item CUX1
#' \item E2F4
#' \item E2F6
#' \item EBF1
#' \item EGR1
#' \item ELF1
#' \item ELK1
#' \item EP300
#' \item ESRRA
#' \item ETS1
#' \item EZH2
#' \item FOSL1
#' \item FOSL2
#' \item FOS
#' \item FOXA1
#' \item FOXA2
#' \item FOXM1
#' \item GABPA
#' \item GATA2
#' \item GATA3
#' \item GTF2F1
#' \item HA
#' \item HDAC2
#' \item HDAC6
#' \item HNF4A
#' \item HNF4G
#' \item IRF3
#' \item IRF4
#' \item JUND
#' \item JUN
#' \item KAT2A
#' \item KAT2B
#' \item KDM1A
#' \item KDM4A
#' \item KDM5A
#' \item KDM5B
#' \item MAFF
#' \item MAFK
#' \item MAX
#' \item MAZ
#' \item MBD4
#' \item MEF2A
#' \item MEF2C
#' \item MTA3
#' \item MXI1
#' \item MYBL2
#' \item MYC
#' \item NANOG
#' \item NCOR1
#' \item NFATC1
#' \item NFIC
#' \item NR2F2
#' \item NR3C1
#' \item NRF1
#' \item PAX5
#' \item PBX3
#' \item PHF8
#' \item PML
#' \item POU2F2
#' \item PRDM1
#' \item RAD21
#' \item RBBP5
#' \item RCOR1
#' \item REST
#' \item RFX5
#' \item RNF2
#' \item RUNX3
#' \item RXRA
#' \item SAP30
#' \item SETDB1
#' \item SIN3A
#' \item SIRT6
#' \item SIX5
#' \item SMC3
#' \item SP1
#' \item SP2
#' \item SP4
#' \item SPI1
#' \item SREBF1
#' \item SREBF2
#' \item SRF
#' \item STAT3
#' \item STAT5A
#' \item SUPT20H
#' \item SUZ12
#' \item TAF1
#' \item TAF7
#' \item TAL1
#' \item TBP
#' \item TCF12
#' \item TCF3
#' \item TEAD4
#' \item USF1
#' \item USF2
#' \item WRNIP1
#' \item YY1
#' \item ZBTB33
#' \item ZBTB7A
#' \item ZC3H11A
#' \item ZEB1
#' \item ZMIZ1
#' \item ZNF143
#' \item ZNF274
#' \item ZNF384
#' }
#'
#' @docType data
#'
#' @keywords metagene profiles
#' @keywords compendium
#' @keywords Transcription factors
#'
#' @usage data(compendium_profiles_TF)
#'
#' @format A list of data frames with the coordinates of the
#' metagene profile of the respective transcription factor.
#'
#' x : genomic coordinates
#' mean : the mean of the signal intensity in the compendium
#' sd : the standard deviation of the signal intensity in the
#' compendium
#' q1..q5 : being the respective quantile of the value distribution
#' sderr : standard error
#' setSize : setsize analysed
#'
#' @source XX
#'
"compendium_profiles_TF"
carmencita/ChIC.data documentation built on April 29, 2021, 8:55 a.m.
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
#' Histone mark compendium
#'
#' Histone mark ChIP-seq compendium for the ChIC package.
#' The compendium contains quality control metrics and metadata for 2204
#' histone mark samples
#' analysed from ENCODE and Roadmap Epigenomics.
#'
#' @docType data
#'
#' @keywords histone marks
#' @keywords quality control metrics
#' @keywords compendium
#'
#' @usage data(compendium_db)
#'
#' @format Data frame with 251 variables (quality control metrics, metadata)
#' for each analysed sample.
#'
#' @source XX
#'
"compendium_db"
#' Transcription factor compendium
#'
#' Transcription factor ChIP-seq compendium for the ChIC package.
#' The compendium contains quality control metrics and metadata for 1350
#' transcription factors analysed from ENCODE.
#'
#'
#' @docType data
#'
#' @keywords tf
#' @keywords quality control metrics
#' @keywords compendium
#'
#' @usage data(compendium_db_tf)
#'
#' @format Data frame with 251 variables (quality control metrics, metadata)
#' for each analysed sample.
#'
#' @source XX
#'
"compendium_db_tf"
#' List with definitions
#'
#' List containing information about chromatin marks, transcription
#' factors, definitions for broad and sharp class.
#'
#' @docType data
#'
#' @keywords definitions
#'
#' @usage data(classesDefList)
#' @import caret
#' @format A list of 5, containing a vector with chromatin mark names,
#' TF names, the members of sharp binding marks, broad binding marks
#' and RNApol2
#'
#' \itemize{
#' \item Hlist: vector with chromatin marks
#' \item allSharp: vector with sharp binding marks
#' \item allBroad: vector with broad binding marks
#' \item RNAPol2 : RNApol2
#' \item TF: vector with TF names
#'}
#'
"classesDefList"
#' Random forest models for chromatin marks ChIP-seq
#' experiment classification
#'
#' Random forest models based on ENCODE and Roadmap data for ChIP-seq
#' experiment classification using the ChIC package.
#'
#' @docType data
#'
#' @keywords classification
#'
#' @usage data(rf_models)
#' @import caret
#' @import randomForest
#' @format A list of 7 random forest models for the different
#' chromatin marks and transcription factors:
#'
#' \itemize{
#' \item Broad : model for broad binding marks
#' \item H3K9me3 : model for H3K9me3
#' \item H3K27me3 : model for H3K27me3
#' \item H3K36me3 : model for H3K36me3
#' \item RNAPol2 : model for RNAPol2
#' \item Sharp : model for sharp binding marks
#' \item TF : model for transcription factors
#'}
#'
"rf_models"
#' Example results from the qualityScores_EM() function based on the example ChIP-seq data for the Vignette for ChIC package
#'
#' Example data to be used in the vignette for ChIC package
#'
#' @docType data
#'
#' @keywords EM_Results
#'
#' @usage data(EM_Results)
#' @format list containing EM scores and filtered reads
#'
#'
"EM_Results"
#' ChIP-seq bam file stored as spp tag-list for
#' a subset of chromosomes for the chip
#'
#' Example data for manual and vignette.
#' tag-list created with the
#' read.bam.tags() function from spp package.
#' The original bam file has been dowloaded from ENCODE
#' (ID: ENCFF000BFX).
#'
#' @docType data
#'
#' @keywords bamfile
#'
#' @usage data(chipSubset)
#' @format list of 2 elements containing the reads and the
#' read quality of the ChIP.
#'
#' \itemize{
#' \item tags : list containing the start coordinates
#' of each read aligned (ChIP) (3'end)
#' \item quality: list containing the read quality
#' of each read
#'}
#'
"chipSubset"
#' ChIP-seq bam file stored as spp tag-list for
#' a subset of chromosomes for the input
#'
#' Example data for manual and vignette.
#' Tag-list created with the
#' read.bam.tags() function from spp package for
#' the input data.
#' The original bam file has been dowloaded from ENCODE
#' (ID: ENCFF000BDQ).
#'
#' @docType data
#'
#' @keywords bamfile
#'
#' @usage data(inputSubset)
#' @format list of 2 elements containing the reads and the
#' read quality of the input.
#'
#' \itemize{
#' \item tags : list containing the start coordinates
#' of each read aligned (input) (3'end)
#' \item quality: list containing the read quality
#' of each read
#'}
#'
"inputSubset"
##profile compendiums
#' Metagene profile data for chromatin marks
#'
#' Compendium of averaged metagene profiles for the ChIC package. Contains
#' averaged metagene profiles for following ChIP-seq datasets from ENCODE
#' and Roadmap Epigenomics.
#'
#' \itemize{
#' \item H2A.Z
#' \item H2AFZ
#' \item H2AK5ac
#' \item H2AK9ac
#' \item H2BK120ac
#' \item H2BK12ac
#' \item H2BK15ac
#' \item H2BK20ac
#' \item H2BK5ac
#' \item H3K14ac
#' \item H3K18ac
#' \item H3K23ac
#' \item H3K23me2
#' \item H3K27ac
#' \item H3K27me3
#' \item H3K36me3
#' \item H3K4ac
#' \item H3K4me1
#' \item H3K4me2
#' \item H3K4me3
#' \item H3K56ac
#' \item H3K79me1
#' \item H3K79me2
#' \item H3K9ac
#' \item H3K9me1
#' \item H3K9me3
#' \item H3T11ph
#' \item H4K12ac
#' \item H4K20me1
#' \item H4K5ac
#' \item H4K8ac
#' \item H4K91ac
#' \item POLR2A
#' \item POLR2AphosphoS2
#' \item POLR2AphosphoS5
#' }
#'
#' @docType data
#'
#' @keywords metagene profiles
#' @keywords compendium
#' @keywords chromatin marks
#'
#' @usage data(compendium_profiles)
#'
#' @format A list of data frames with the coordinates of the
#' metagene profile of the respective chromatin mark.
#'
#' x : genomic coordinates
#' mean : the mean of the signal intensity in the compendium
#' sd : the standard deviation of the signal intensity in the
#' compendium
#' q1..q5 : being the respective quantile of the value distribution
#' sderr : standard error
#' setSize : setsize analysed
#' @source XX
#'
"compendium_profiles"
#' Metagene profile data for transcription factors
#'
#' Compendium of averaged metagene profiles for the ChIC package. Contains
#' averaged metagene profiles for following ChIP-seq datasets from ENCODE.
#'
#' \itemize{
#' \item ARID3A
#' \item ATF2
#' \item ATF3
#' \item BACH1
#' \item BATF
#' \item BCL11A
#' \item BCL3
#' \item BCLAF1
#' \item BHLHE40
#' \item BRCA1
#' \item CBX2
#' \item CBX3
#' \item CEBPB
#' \item CEBPD
#' \item CEBPZ
#' \item CHD1
#' \item CHD2
#' \item CHD4
#' \item CREB1
#' \item CREBBP
#' \item CTCF
#' \item CUX1
#' \item E2F4
#' \item E2F6
#' \item EBF1
#' \item EGR1
#' \item ELF1
#' \item ELK1
#' \item EP300
#' \item ESRRA
#' \item ETS1
#' \item EZH2
#' \item FOSL1
#' \item FOSL2
#' \item FOS
#' \item FOXA1
#' \item FOXA2
#' \item FOXM1
#' \item GABPA
#' \item GATA2
#' \item GATA3
#' \item GTF2F1
#' \item HA
#' \item HDAC2
#' \item HDAC6
#' \item HNF4A
#' \item HNF4G
#' \item IRF3
#' \item IRF4
#' \item JUND
#' \item JUN
#' \item KAT2A
#' \item KAT2B
#' \item KDM1A
#' \item KDM4A
#' \item KDM5A
#' \item KDM5B
#' \item MAFF
#' \item MAFK
#' \item MAX
#' \item MAZ
#' \item MBD4
#' \item MEF2A
#' \item MEF2C
#' \item MTA3
#' \item MXI1
#' \item MYBL2
#' \item MYC
#' \item NANOG
#' \item NCOR1
#' \item NFATC1
#' \item NFIC
#' \item NR2F2
#' \item NR3C1
#' \item NRF1
#' \item PAX5
#' \item PBX3
#' \item PHF8
#' \item PML
#' \item POU2F2
#' \item PRDM1
#' \item RAD21
#' \item RBBP5
#' \item RCOR1
#' \item REST
#' \item RFX5
#' \item RNF2
#' \item RUNX3
#' \item RXRA
#' \item SAP30
#' \item SETDB1
#' \item SIN3A
#' \item SIRT6
#' \item SIX5
#' \item SMC3
#' \item SP1
#' \item SP2
#' \item SP4
#' \item SPI1
#' \item SREBF1
#' \item SREBF2
#' \item SRF
#' \item STAT3
#' \item STAT5A
#' \item SUPT20H
#' \item SUZ12
#' \item TAF1
#' \item TAF7
#' \item TAL1
#' \item TBP
#' \item TCF12
#' \item TCF3
#' \item TEAD4
#' \item USF1
#' \item USF2
#' \item WRNIP1
#' \item YY1
#' \item ZBTB33
#' \item ZBTB7A
#' \item ZC3H11A
#' \item ZEB1
#' \item ZMIZ1
#' \item ZNF143
#' \item ZNF274
#' \item ZNF384
#' }
#'
#' @docType data
#'
#' @keywords metagene profiles
#' @keywords compendium
#' @keywords Transcription factors
#'
#' @usage data(compendium_profiles_TF)
#'
#' @format A list of data frames with the coordinates of the
#' metagene profile of the respective transcription factor.
#'
#' x : genomic coordinates
#' mean : the mean of the signal intensity in the compendium
#' sd : the standard deviation of the signal intensity in the
#' compendium
#' q1..q5 : being the respective quantile of the value distribution
#' sderr : standard error
#' setSize : setsize analysed
#'
#' @source XX
#'
"compendium_profiles_TF"
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