R/extdata.R

In acnr: Annotated Copy-Number Regions

#' Annotated copy-number regions from the GEO GSE29172 (and GSE26302) data sets.
#' 
#' The GEO GSE29172 data set is a dilution series from the Affymetrix 
#' GenomeWideSNP_6 chip type. The GEO GSE26302 data set contains the experiment 
#' corresponding to the matched normal (i.e. 0\% dilution).
#' 
#' These data have been processed from the files available from GEO using 
#' scripts that are included in the 'inst/preprocessing/GSE29172' directory of
#' this package. This processing includes normalization of the raw CEL files
#' using the CRMAv2 method implemented in the aroma.affymetrix package.
#' 
#' @name GSE29172_H1395
#' @format A data frame with 770668 observations of 7 variables: \describe{ 
#'   \item{c}{total copy number (not log-scaled)} \item{b}{allelic ratios in the
#'   diluted tumor sample (after TumorBoost)} \item{genotype}{germline 
#'   genotypes} \item{bT}{allelic ratios in the diluted tumor sample (before 
#'   TumorBoost)} \item{bN}{allelic ratios in the matched normal sample} 
#'   \item{region}{a character value, annotation label for the region. Should be
#'   encoded as \code{"(C1,C2)"}, where \code{C1} denotes the minor copy number 
#'   and \code{C2} denotes the major copy number.  For example, \describe{ 
#'   \item{(1,1)}{Normal} \item{(0,1)}{Hemizygous deletion} 
#'   \item{(0,0)}{Homozygous deletion} \item{(1,2)}{Single copy gain} 
#'   \item{(0,2)}{Copy-neutral LOH} \item{(2,2)}{Balanced two-copy gain} 
#'   \item{(1,3)}{Unbalanced two-copy gain} \item{(0,3)}{Single-copy gain with 
#'   LOH} } } \item{genotype}{the (germline) genotype of SNPs. By definition, rows 
#'   with missing genotypes are interpreted as non-polymorphic loci (a.k.a. copy
#'   number probes).} \item{cellularity}{A numeric value between 0 and 1, the
#'   percentage of tumor cells in the  sample.} }
#' @source \url{http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29172} 
#' \url{http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE26302}
#' 
#' @references Rasmussen, M., Sundstr\"om, M., Kultima, H. G., Botling, J., 
#'   Micke, P., Birgisson, H., Glimelius, B. & Isaksson, A. (2011). 
#'   Allele-specific copy number analysis of tumor samples with aneuploidy and 
#'   tumor heterogeneity. Genome Biology, 12(10), R108.#'
#'   
#' @references Bengtsson, H., Wirapati , P. & Speed, T.P. (2009). A single-array
#'   preprocessing method for estimating full-resolution raw copy numbers from 
#'   all Affymetrix genotyping arrays including GenomeWideSNP 5 & 6, 
#'   Bioinformatics 25(17), pp. 2149-56.
#'   
#' @references Bengtsson H., Neuvial, P. and Speed, T. P. (2010) TumorBoost:
#'   normalization of allele-specific tumor copy numbers from a single pair of
#'   tumor-normal genotyping microarrays. BMC bioinformatics 11 (2010), p. 245.
#'   
#' @examples
#' dat <- loadCnRegionData("GSE29172_H1395")
#' unique(dat$region)
NULL

#' Annotated copy-number regions from the GEO GSE11976 data set.
#' 
#' The GEO GSE11976 data set is a dilution series from the Illumina 
#' HumanCNV370v1 chip type (Staaf et al, 2008).
#' 
#' These data have been processed from the files available at 
#' http://cbbp.thep.lu.se/~markus/software/BAFsegmentation/ using scripts that 
#' are included in the 'inst/preprocessing/GSE11976' directory of this package.
#' 
#' @name GSE11976_CRL2324
#' @format A data frame with 770668 observations of 7 variables: 
#' \describe{ 
#'   \item{c}{total copy number (not log-scaled)} 
#'   \item{b}{allelic ratios in the
#'   diluted tumor sample (after TumorBoost)} 
#'   \item{genotype}{germline
#'   genotypes} 
#'   \item{region}{a character value, annotation label for the region. Should be
#'   encoded as \code{"(C1,C2)"}, where \code{C1} denotes the minor copy number
#'   and \code{C2} denotes the major copy number.  For example, 
#'   \describe{ 
#'   \item{(1,1)}{Normal} \item{(0,1)}{Hemizygous deletion} 
#'   \item{(0,0)}{Homozygous deletion} \item{(1,2)}{Single copy gain} 
#'   \item{(0,2)}{Copy-neutral LOH} \item{(2,2)}{Balanced two-copy gain} 
#'   \item{(1,3)}{Unbalanced two-copy gain} \item{(0,3)}{Single-copy gain with
#'   LOH} } }
#'   \item{cellularity}{A numeric value between 0 and 1, the percentage of tumor cells in the  sample.}
#'   }
#'  @source http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE11976
#'  @references Staaf, J., Lindgren, D., Vallon-Christersson, J., Isaksson, A., 
#'  Goransson, H., Juliusson, G., ... & Ringn\'er, M. (2008). 
#'  Segmentation-based detection of allelic imbalance and 
#'  loss-of-heterozygosity in cancer cells using whole genome SNP arrays. 
#'  Genome Biol, 9(9), R136.
#' @examples
#' dat <- loadCnRegionData("GSE11976_CRL2324")
#' unique(dat$region)
NULL


#' Annotated copy-number regions from the GEO GSE13372 data set.
#' 
#' The GEO GSE13372 data set is from the Affymetrix GenomeWideSNP_6 chip type. 
#' We have extracted one tumor/normal pair corresponding to the breast cancer 
#' cell line HCC1143. For consistency with the other data sets in the package 
#' the tumor and normal samples are labeled according to their tumor 
#' cellularity, that is, 100% and 0% cellularity, respectively.
#' 
#' These data have been processed from the files available from GEO using 
#' scripts that are included in the 'inst/preprocessing/GSE13372' directory of 
#' this package. This processing includes normalization of the raw CEL files 
#' using the CRMAv2 method implemented in the aroma.affymetrix package.
#' 
#' @name GSE13372_HCC1143
#' @format A data frame with 205842 observations of 7 variables: \describe{ 
#'   \item{c}{total copy number (not log-scaled)} \item{b}{allelic ratios in the
#'   diluted tumor sample (after TumorBoost)} \item{genotype}{germline 
#'   genotypes} \item{bT}{allelic ratios in the diluted tumor sample (before 
#'   TumorBoost)} \item{bN}{allelic ratios in the matched normal sample} 
#'   \item{region}{a character value, annotation label for the region. Should be
#'   encoded as \code{"(C1,C2)"}, where \code{C1} denotes the minor copy number 
#'   and \code{C2} denotes the major copy number.  For example, \describe{ 
#'   \item{(1,1)}{Normal} \item{(0,1)}{Hemizygous deletion} 
#'   \item{(0,0)}{Homozygous deletion} \item{(1,2)}{Single copy gain} 
#'   \item{(0,2)}{Copy-neutral LOH} \item{(2,2)}{Balanced two-copy gain} 
#'   \item{(1,3)}{Unbalanced two-copy gain} \item{(0,3)}{Single-copy gain with 
#'   LOH} } } \item{genotype}{the (germline) genotype of SNPs. By definition, 
#'   rows with missing genotypes are interpreted as non-polymorphic loci (a.k.a.
#'   copy number probes).} \item{cellularity}{A numeric value between 0 and 1, 
#'   the percentage of tumor cells in the sample.} }
#' @source \url{http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE13372} 
#'   \url{http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE13372}
#'   
#' @references Chiang DY, Getz G, Jaffe DB, O'Kelly MJ et al. High-resolution
#'   mapping of copy-number alterations with massively parallel sequencing. Nat
#'   Methods 2009 Jan;6(1):99-103. PMID: 19043412

#' 
#' @references Bengtsson, H., Wirapati , P. & Speed, T.P. (2009). A single-array
#'   preprocessing method for estimating full-resolution raw copy numbers from 
#'   all Affymetrix genotyping arrays including GenomeWideSNP 5 & 6, 
#'   Bioinformatics 25(17), pp. 2149-56.
#'   
#' @references Bengtsson H., Neuvial, P. and Speed, T. P. (2010) TumorBoost: 
#'   normalization of allele-specific tumor copy numbers from a single pair of 
#'   tumor-normal genotyping microarrays. BMC bioinformatics 11 (2010), p. 245.
#'   
#' @examples
#' dat <- loadCnRegionData("GSE13372_HCC1143")
#' unique(dat$region)

NULL