Annotated data sets contained in the `acnr` package

In acnr: Annotated Copy-Number Regions

library("knitr")
opts_chunk$set(
dev='png', fig.width=5, fig.height=5
)

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

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)

Session information

sessionInfo()

acnr documentation built on May 2, 2019, 9:25 a.m.