Import CCLE copy number data

CCLECopyNumberData(
  dataset = c("depmap_public_21q2", "depmap_public_21q1", "depmap_public_20q4v2",
    "depmap_public_20q3", "depmap_public_20q2", "depmap_public_20q1")
)

Arguments

dataset	`character(1)`. DepMap dataset release name.

Value

CCLECopyNumberData.

Note

Updated 2021-07-07.

Examples

object <- CCLECopyNumberData()
#> → Downloading DepMap file <https://ndownloader.figshare.com/files/27902124>.
#> → Importing /Users/mike/.cache/R/DepMapAnalysis/f5403d1f8a3f_27902124 using data.table::`fread()`.
#> → Downloading Homo sapiens gene info from NCBI at <ftp://ftp.ncbi.nih.gov/gene/DATA/GENE_INFO/Mammalia/Homo_sapiens.gene_info.gz>.
#> → Importing /Users/mike/.cache/R/AcidGenomes/50321924c0cb_Homo_sapiens.gene_info.gz using data.table::`fread()`.
#> ! 45 retired NCBI Entrez identifiers in data set: AKAP2_11217, C10orf113_387638, C12orf74_338809, C16orf47_388289, C17orf47_284083, C2orf48_348738.....
#> → Downloading DepMap file <https://ndownloader.figshare.com/files/27902376>.
#> → Importing /Users/mike/.cache/R/DepMapAnalysis/66871289d630_27902376 using data.table::`fread()`.
print(object)
#> class: CCLECopyNumberData 
#> dim: 27517 1742 
#> metadata(8): dataset date ... wd yaml
#> assays(1): log2CopyNumber
#> rownames(27517): A1BG_1 A1BG_AS1_503538 ... ZZEF1_23140 ZZZ3_26009
#> rowData names(13): chromosome dbXrefs ... typeOfGene xTaxId
#> colnames(1742): ACH_000001 ACH_000002 ... ACH_002511 ACH_002512
#> colData names(26): achillesNReplicates age ... subtype wtsiMasterCellId