Annotated data sets contained in the acnr package
Author: M. Pierre-Jean, P. Neuvial
Date: 2017-04-18

# Annotated data sets contained in the `acnr` package

#### M. Pierre-Jean, P. Neuvial

#### 2017-04-18

The `acnr` package is a data package containing SNP array data from different platforms (Affymetrix and Immumina) and different types of copy-number regions. These regions were identified manually by the authors of the package and may be used to generate realistic data sets with known truth.

This package was initially built to serve as a data package for the `jointseg` package which is currently available from github.

Currently the `acnr` package contains three data sets curated from GEO:

    library("acnr")
    dataSets <- listDataSets()
    dataSets

    ## [1] "GSE11976_CRL2324" "GSE13372_HCC1143" "GSE29172_H1395"

This vignette provides basic summary statistics of these data sets.

## Description of the annotated data sets

    tf <- 1
    regList <- lapply(dataSets, FUN=function(ds) {
        regDat <- loadCnRegionData(dataSet=ds, tumorFraction=tf)
        regs <- regDat[["region"]]
    })
    names(regList) <- dataSets

    allregs <- unique(unlist(regList))
    tab <- sapply(allregs, FUN=function(reg) {
        sapply(regList, FUN=function(rr) sum(rr==reg))
    })
    cap <- paste("Size of annotated copy-number regions for each of the",
                length(dataSets), "data sets.")
    knitr::kable(tab, caption=cap)

Size of annotated copy-number regions for each of the 3 data sets.
| (0,0) | (0,1) | (0,2) | (0,3) | (1,1) | (1,2) | (2,2) | (1,3) | (2,3)
--- | --- | --- | --- | --- | --- | --- | --- | --- | ---
GSE11976_CRL2324 | 838 | 2491 | 5480 | 6537 | 3192 | 2744 | 3040 | 0 | 0
GSE13372_HCC1143 | 0 | 8175 | 14798 | 0 | 16856 | 15087 | 0 | 0 | 0
GSE29172_H1395 | 0 | 5000 | 5000 | 5000 | 5000 | 5000 | 5000 | 5000 | 5000

## Session information

    sessionInfo()

    ## R version 3.3.2 RC (2016-10-26 r71594)
    ## Platform: x86_64-apple-darwin13.4.0 (64-bit)
    ## Running under: OS X El Capitan 10.11.6
    ##
    ## locale:
    ## [1] C/fr_FR.UTF-8/fr_FR.UTF-8/C/fr_FR.UTF-8/fr_FR.UTF-8
    ##
    ## attached base packages:
    ## [1] stats     graphics  grDevices utils     datasets  methods   base
    ##
    ## other attached packages:
    ## [1] acnr_1.0.0   knitr_1.15.1
    ##
    ## loaded via a namespace (and not attached):
    ##  [1] backports_1.0.4 magrittr_1.5    rprojroot_1.1   htmltools_0.3.5
    ##  [5] tools_3.3.2     yaml_2.1.14     Rcpp_0.12.8     stringi_1.1.2
    ##  [9] rmarkdown_1.2   highr_0.6       stringr_1.1.0   digest_0.6.12
    ## [13] evaluate_0.10