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Check that specified identifier values exist in the data.

Source: R/validate_identifiers.R
validate_identifiers.Rd

Check that specified identifier values exist in the data and error otherwise.

Usage

validate_identifiers(
  df,
  identifiers = NULL,
  req_ids = NULL,
  exp_one_ids = NULL
)

Arguments

df

data.table with colnames.

identifiers

Named list of identifiers where the names are standardized identifier names. If not passed, defaults to get_env_identifiers().

req_ids

Character vector of standardized identifier names required to pass identifier validation.

exp_one_ids

Character vector of standardized identifiers names where only one identifier value is expected. If not passed, defaults to get_expect_one_identifiers().

Value

Named list of identifiers modified to pass validation against the input data. Errors with explanatory message if validation cannot pass with the given identifiers and data.

Details

Note that this does NOT set the identifiers anywhere (i.e. environment or SummarizedExperiment object). If identifiers do not validate, will throw error as side effect.

Examples

validate_identifiers(
  S4Vectors::DataFrame("Barcode" = NA, "Duration" = NA, "Template" = NA, "clid" = NA), 
  req_ids = "barcode"
)
#> $duration
#> [1] "Duration"
#> 
#> $cellline
#> [1] "clid"
#> 
#> $cellline_name
#> [1] "CellLineName"
#> 
#> $cellline_tissue
#> [1] "Tissue"
#> 
#> $cellline_ref_div_time
#> [1] "ReferenceDivisionTime"
#> 
#> $cellline_parental_identifier
#> [1] "parental_identifier"
#> 
#> $cellline_subtype
#> [1] "subtype"
#> 
#> $drug
#> [1] "Gnumber"
#> 
#> $drug_name
#> [1] "DrugName"
#> 
#> $drug_moa
#> [1] "drug_moa"
#> 
#> $untreated_tag
#> [1] "vehicle"   "untreated"
#> 
#> $masked_tag
#> [1] "masked"
#> 
#> $well_position
#> [1] "WellRow"    "WellColumn"
#> 
#> $concentration
#> [1] "Concentration"
#> 
#> $template
#> [1] "Template"
#> 
#> $barcode
#> [1] "Barcode"
#> 
#> $drug2
#> [1] "Gnumber_2"
#> 
#> $drug_name2
#> [1] "DrugName_2"
#> 
#> $drug_moa2
#> [1] "drug_moa_2"
#> 
#> $concentration2
#> [1] "Concentration_2"
#> 
#> $drug3
#> [1] "Gnumber_3"
#> 
#> $drug_name3
#> [1] "DrugName_3"
#> 
#> $drug_moa3
#> [1] "drug_moa_3"
#> 
#> $concentration3
#> [1] "Concentration_3"
#> 
#> $data_source
#> [1] "data_source"
#> 
#> $replicate
#> [1] "Replicate"
#> 
#> $normalization_type
#> [1] "normalization_type"
#>