Annotated data sets contained in the acnr package

Description of the annotated data sets

tf <- 1
dataSets <- listDataSets()

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.")
if (require(xtable)) {
    print(xtable(tab, caption=cap, label="tab:regData",
                table.placement="!h", caption.placement="bottom"))
}

## Loading required package: xtable

## % latex table generated in R 4.4.2 by xtable 1.8-4 package
## % Thu Nov 14 05:14:30 2024
## \begin{table}[ht]
## \centering
## \begin{tabular}{rrrrrrrrrr}
##   \hline
##  & (0,0) & (0,1) & (0,2) & (0,3) & (1,1) & (1,2) & (2,2) & (1,3) & (2,3) \\ 
##   \hline
## 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 & 22615 & 24135 & 25405 & 21539 & 19048 & 27924 & 20903 & 31098 \\ 
##    \hline
## \end{tabular}
## \caption{Size of annotated copy-number regions for each of the 3 data sets.} 
## \label{tab:regData}
## \end{table}

Session information

sessionInfo()

## R version 4.4.2 (2024-10-31)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.1 LTS
## 
## Matrix products: default
## BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 
## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.26.so;  LAPACK version 3.12.0
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=C              
##  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
##  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
## 
## time zone: Etc/UTC
## tzcode source: system (glibc)
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] xtable_1.8-4      knitr_1.49        R.utils_2.12.3    R.oo_1.27.0      
## [5] R.methodsS3_1.8.2 acnr_0.3.2        rmarkdown_2.29   
## 
## loaded via a namespace (and not attached):
##  [1] digest_0.6.37     R6_2.5.1          fastmap_1.2.0     xfun_0.49        
##  [5] maketools_1.3.1   cachem_1.1.0      htmltools_0.5.8.1 buildtools_1.0.0 
##  [9] lifecycle_1.0.4   cli_3.6.3         sass_0.4.9        jquerylib_0.1.4  
## [13] compiler_4.4.2    sys_3.4.3         tools_4.4.2       evaluate_1.0.1   
## [17] bslib_0.8.0       yaml_2.3.10       jsonlite_1.8.9    rlang_1.1.4