R/documentData.R

In b-klaus/DChIPRep: DChIPRep - Analysis of chromatin modification ChIP-Seq data with replication

#' A test DESeqDataSet
#'
#' test data to check the functions
#'
#' @usage data(testData)
#' @format a DESeqDataSet
#' @return a DESeqDataSet
"testData"

#' An example sample table data.frame
#'
#' An example sample table
#'
#' @usage data(exampleSampleTable)
#'
#' @format a data.frame
#' @return a data.frame
#' @seealso \link{exampleChipData} \link{exampleInputData}
"exampleSampleTable"

#' An example input data.
#'
#' An example input data set that can be used with
#' \code{\link{importDataFromMatrices}}.
#' Its associated sample table can be accessed via
#' data(data(exampleSampleTable).
#'
#'
#' @usage data(exampleInputData)
#'
#' @format a matrix
#' @return a matrix
#' @seealso \link{exampleSampleTable} \link{exampleChipData}
"exampleInputData"


#' An example ChIP data.
#'
#' An example ChIP data set that can be used with
#' \code{\link{importDataFromMatrices}}.
#' Its associated sample table can be accessed via 
#' data(data(exampleSampleTable).
#'
#' @usage data(exampleChipData)
#'
#' @format a matrix
#' @return a matrix
#' @seealso \link{exampleSampleTable} \link{exampleInputData}
"exampleChipData"


#' TSS around called peak regions from Galonska et. al.
#'
#' This data contains mouse mm9 TSS close to called peak regions for H3Kme3 
#' from Galonksa
#' et al. The original peak lists are from are from GEO (GSE56312) and have been
#' merged into a common peaklist and then annotated to the closest mm9 TSS using
#' \link[ChIPpeakAnno]{annotatePeakInBatch}.
#'
#' @usage data(exampleChipData)
#'
#' @import ChIPpeakAnno
#'
#' @format an annoGR object from the package \code{ChIPpeakAnno}.
#' @return an annoGR object from the package \code{ChIPpeakAnno}.
#' @seealso \link{chip_galonska} \link{input_galonska} \link{sample_table_galonska}
"TSS_galonska"



#' Another example ChIP data set that can be used 
#' with \code{\link{importDataFromMatrices}} from rom Galonska et. al., 2015.
#'
#' The containes the H3Kme3 data in the serum and 24h_2i conditions 
#' from Galonska et. al., 2015
#' as well as the whole cell extract data, which is treated as input for all
#' four samples.
#' The data were downloaded from the SRA at the european
#' nucleotide archive (ENA, accession PRJNA242892).
#' The reads were aligned ot the mm9 reference genome using bowtie2
#' (Langmead and Salzberg, 2012) with
#' default options. Then, filtering of unmapped, low mapping quality (< 10), 
#' duplicated and
#' multi-mapping reads was performed with Picard tools.
#' The fragment length was inferred using
#' cross correlation plots from SPP (Kharchenko, et. al., 2008).
#'
#' @references
#'
#' Galonska, Christina, Michael J. Ziller, Rahul Karnik, and Alexander 
#' Meissner. 2015. "Ground State Conditions Induce Rapid Reorganization of 
#' Core Pluripotency Factor Binding Before Global Epigenetic Reprogramming." 
#' Cell Stem Cell 17 (4). Elsevier BV: 462-70.
#' \url{http://dx.doi.org/10.1016/j.stem.2015.07.005}.

#'Kharchenko, Peter V, Michael Y Tolstorukov, and Peter J Park. 2008. 
#'"Design and Analysis of ChIP-Seq Experiments for DNA-Binding Proteins."
#' Nat Biotechnol 26 (12). Nature Publishing Group: 1351-9. 
#'\url{http://dx.doi.org/10.1038/nbt.1508}.

#'Langmead, Ben, and Steven L Salzberg. 2012. 
#'"Fast Gapped-Read Alignment with Bowtie 2." 
#' Nature Methods 9 (4). Nature Publishing Group: 357-59. 
#'\url{http://dx.doi.org/10.1038/nmeth.1923}.

#'Picard Tools - by Broad Institute. 2016.
#' \url{http://broadinstittue.github.io/picard/}.

#'
#' @usage data(chip_galonska)
#'
#' @format a matrix
#' @return a matrix
#' @seealso \link{sample_table_galonska} \link{input_galonska} \link{TSS_galonska}
"chip_galonska"

#' Another example Input data set that can be used 
#' with \code{\link{importDataFromMatrices}} from rom Galonska et. al., 2015.
#'
#' The matrix containes the whole cell extract (WCE) data for H3Kme3 
#' from the paper
#' in each of the four columns, since
#' this is the only inpu data provided for all 4 samples. For additional
#' information see the documentation
#' of \link{chip_galonska}.
#'
#' @usage data(input_galonska)
#'
#' @format a matrix
#' @return a matrix
#' @seealso \link{chip_galonska} \link{sample_table_galonska} \link{TSS_galonska}
"input_galonska"

#' Another example sample table based on data  from rom Galonska et. al., 2015.
#'
#' This table contains the sample annotation for the H3Kme3 data from
#' Galonska et. al., 2015. For additional information see the documentation
#' of \link{chip_galonska}.
#'
#' @usage data(sample_table_galonska)
#'
#' @format a data.frame
#' @return a data.frame
#' @seealso \link{chip_galonska} \link{input_galonska} \link{TSS_galonska}
"sample_table_galonska"