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#' 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
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