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identify_keys

Source: R/identify_keys.R
identify_keys.Rd

Group columns from a data.table that correspond to different

Usage

identify_keys(
  df_,
  nested_keys = NULL,
  override_untrt_controls = NULL,
  identifiers = gDRutils::get_env_identifiers()
)

Arguments

df_

a data.table to identify keys for.

nested_keys

character vector of keys to exclude from the returned list. The keys discarded should be identical to the keys in the third dimension of the SummarizedExperiment. Defaults to the "Barcode" and the masked identifier.

override_untrt_controls

named list containing defining factors in the treatments. Defaults to NULL.

identifiers

named list containing all identifiers to use during processing. By default, this value will be obtained by the environment.

Value

named list of key types and their corresponding key values.

Details

This is most likely to be used for provenance tracking and will be placed on the SummarizedExperiment metadata for downstream analyses to reference.

See also

map_df, create_SE

Examples

n <- 64
md_df <- data.table::data.table(
  Gnumber = rep(c("vehicle", "untreated", paste0("G", seq(2))), each = 16), 
  DrugName = rep(c("vehicle", "untreated", paste0("GN", seq(2))), each = 16), 
  clid = paste0("C", rep_len(seq(4), n)),
  CellLineName = paste0("N", rep_len(seq(4), n)),
  replicates = rep_len(paste0("R", rep(seq(4), each = 4)), 64),
  drug_moa = "inhibitor",
  ReferenceDivisionTime = rep_len(c(120, 60), n),
  Tissue = "Lung",
  parental_identifier = "CL12345",
  Duration = 160
)
md_df <- unique(md_df)
ref <- md_df$Gnumber %in% c("vehicle", "untreated")
trt_df <- md_df[!ref, ]
identify_keys(trt_df)
#> $Trt
#> [1] "Gnumber"             "DrugName"            "clid"               
#> [4] "CellLineName"        "replicates"          "drug_moa"           
#> [7] "Tissue"              "parental_identifier" "Duration"           
#> 
#> $ref_Endpoint
#> [1] "clid"                "CellLineName"        "replicates"         
#> [4] "Tissue"              "parental_identifier" "Duration"           
#> 
#> $untrt_Endpoint
#> [1] "clid"                "CellLineName"        "replicates"         
#> [4] "Tissue"              "parental_identifier" "Duration"           
#> 
#> $Day0
#> character(0)
#> 
#> $nested_keys
#> NULL
#> 
#> $masked_tag
#> [1] "masked"
#> 
#> $cellline_name
#> [1] "CellLineName"
#> 
#> $cellline_ref_div_time
#> [1] "ReferenceDivisionTime"
#> 
#> $duration
#> [1] "Duration"
#> 
#> $untreated_tag
#> [1] "vehicle"   "untreated"
#>