Gene effect in cancer cell lines

GeneEffect(
  dataset = c("depmap_public_21q2", "depmap_public_21q1", "depmap_public_20q4v2",
    "depmap_public_20q3", "depmap_public_20q2", "depmap_public_20q1",
    "sanger_project_score_2021_05", "sanger_project_score_2019_08", "demeter2_data_v6"),
  project = "default",
  scoringMethod = "default"
)

Arguments

dataset

character(1). DepMap dataset release name.

project

character(1). Project name. Defaults to a combination of multiple projects ("combined"):

  • CRISPR: Broad DepMap Public, Sanger Project Score (e.g. for depmap_public_21q2).

  • RNAi: Achilles, DRIVE, Marcotte (e.g. for demeter2_data_v6).

scoringMethod

character(1). Scoring method name to use.

  • CRISPR: "chronos" (as of 2021 Q1) or "ceres" (e.g. depmap_public_21q2 dataset).

  • RNAi: "demeter2" (e.g. demeter2_data_v6 dataset).

Value

GeneEffect.

Note

Updated 2021-07-19.

Assays

  • effect: Chronos or CERES data with principle components strongly related to known batch effects removed, then shifted and scaled per cell line so the median nonessential KO effect is 0 and the median essential KO effect is -1.

  • probability: Probability that knocking out the gene has a real depletion effect using gene_effect.

Examples

object <- GeneEffect()
#>
#> ๐Ÿงช # Preparing `depmap_public_21q2` gene effect dataset.
#> libraryType: crispr
#> project: combined
#> releaseDate: 2021-05
#> scoringMethod: chronos
#> โ†’ Downloading DepMap file <https://ndownloader.figshare.com/files/27902229>.
#> โ†’ Importing /Users/mike/.cache/R/DepMapAnalysis/104515ee8e07a_27902229 using data.table::`fread()`.
#> โ†’ Downloading DepMap file <https://ndownloader.figshare.com/files/27902175>.
#> โ†’ Importing /Users/mike/.cache/R/DepMapAnalysis/10451ae99a44_27902175 using data.table::`fread()`.
#> โ†’ Downloading DepMap file <https://ndownloader.figshare.com/files/27902166>.
#> โ†’ Importing /Users/mike/.cache/R/DepMapAnalysis/104515629f2b2_27902166 using base::`read.table()`.
#> โ†’ Downloading DepMap file <https://ndownloader.figshare.com/files/27902160>.
#> โ†’ Importing /Users/mike/.cache/R/DepMapAnalysis/668752e212ca_27902160 using base::`read.table()`.
#> โ†’ Downloading DepMap file <https://ndownloader.figshare.com/files/27902370>.
#> โ†’ Importing /Users/mike/.cache/R/DepMapAnalysis/6687783fb648_27902370 using base::`read.table()`.
#> โ†’ Downloading Homo sapiens gene info from NCBI at <ftp://ftp.ncbi.nih.gov/gene/DATA/GENE_INFO/Mammalia/Homo_sapiens.gene_info.gz>.
#> โ†’ Importing /Users/mike/.cache/R/AcidGenomes/50321924c0cb_Homo_sapiens.gene_info.gz using data.table::`fread()`.
#> ! 8 retired NCBI Entrez identifiers in data set: AKAP2_11217, C10orf113_387638, C12orf74_338809, C17orf47_284083, CRIPAK_285464, KIAA1107_23285, .....
#> โ†’ Downloading DepMap file <https://ndownloader.figshare.com/files/27902376>.
#> โ†’ Importing /Users/mike/.cache/R/DepMapAnalysis/66871289d630_27902376 using data.table::`fread()`.
#> ! 1 missing cell line in `colData`: ACH_002315.
print(object)
#> GeneEffect 0.2.0 of length 17385 #> dataset: depmap_public_21q2 #> libraryType: crispr #> project: combined #> scoringMethod: chronos #> date: 2021-07-19 #> releaseDate: 2021-05 #> class: SummarizedExperiment #> dim: 17385 989 #> metadata(16): commonEssentials controlCommonEssentials ... wd yaml #> assays(2): effect probability #> rownames(17385): A1BG_1 A1CF_29974 ... ZZEF1_23140 ZZZ3_26009 #> rowData names(13): chromosome dbXrefs ... typeOfGene xTaxId #> colnames(989): ACH_000001 ACH_000004 ... ACH_002510 ACH_002512 #> colData names(26): achillesNReplicates age ... subtype wtsiMasterCellId