R/loadCnRegionData.R

In acnr: Annotated Copy-Number Regions

loadCnRegionData <- structure(function(
### Load real, annotated copy number data
    dataSet=c("GSE29172", "GSE11976", "GSE13372"),
### microarray dataSet from which the data was generated.
    tumorFraction=1
### proportion of tumor cells in the "tumor" sample.
### Should be in {.3, .5, .7, 1} if \code{dataSet=="GSE29172"},
### in {0,.14,.34,.50,.79,1} when \code{dataSet=="GSE11976"}.
### and in {0,1} when \code{dataSet=="GSE13372"}.
    ){
    ##details<<This function is a wrapper to load real genotyping array
    ##data taken from dilution series from the Affymetrix
    ##GenomeWideSNP_6 chip type (Rasmussen et al, 2011) or from the
    ##Illumina HumanCNV370v1 chip type (Staaf et al, 2008)
    
    ##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. 
    
    ##references<<GEO data set:
    ##http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE11976
    
    ##references<<Rasmussen, M., Sundstr\"{o}m, 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<<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
    
    ##references<<GEO data sets:
    ##http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29172
    ##http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE26302
    ##http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE13372

    dataSet <- match.arg(dataSet)
    tumorFractions <- switch(dataSet,
                             GSE13372=c(0,1),
                             GSE29172=c(.3, .5, .7, 1),
                             GSE11976=c(0,.14,.34,.50,.79,1))
    if(!(tumorFraction %in% tumorFractions)) {
        stop("'tumorFraction' should be in c(",
             paste(tumorFractions, collapse=", "), ") for dataSet ", dataSet)
    }
    
    sampleName <- switch(dataSet,
                         GSE13372="GSE13372,ASCRMAv2,HCC1143_GLEYSvsHCC1143BL_GLEYS",
                         GSE29172="GSE29172,ASCRMAv2,H1395vsBL1395",
                         GSE11976="CRL2324,BAF")
    chipType <- switch(dataSet,
                       GSE13372="GenomeWideSNP_6",
                       GSE29172="GenomeWideSNP_6",
                       GSE11976="HumanCNV370v1")
    filename <- sprintf("%s,%s,cnRegions.rds", sampleName, 100*tumorFraction)
    relPath <- file.path("extdata", dataSet, chipType, filename)
    pathname <- system.file(relPath, package="acnr")
    readRDS(pathname)
### a data.frame containing copy number data for different types of
### copy number regions.  Columns:\describe{
### \item{c}{Total copy number}
### \item{b}{Allele B fraction (a.k.a. BAF)}
### \item{region}{a character value, annotation label for the
### region.  Preferably 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{muN}{the (germline) genotype of SNPs. By definition, rows with
###  missing genotypes are interpreted as non-polymorphic loci (a.k.a. copy
###  number probes).}}
}, ex=function() {
    affyDat <- loadCnRegionData(dataSet="GSE29172", tumorFraction=1)
    str(affyDat)
    
    illuDat <- loadCnRegionData(dataSet="GSE11976", tumorFraction=.79)
    str(illuDat)
})

############################################################################
## HISTORY:
## 2013-04-13
## o More informative error message when desired tumor fraction is not
## available.
## 2013-01-22
## o Updated doc.
## 2013-01-15
## o Created.
############################################################################