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Remove batch substring from drug id

Source: R/utils.R
remove_drug_batch.Rd

Gnumber, i.e. "G12345678" is currently the default format of drug_id. It's also used as a drug name in some cases.

Usage

remove_drug_batch(
  drug_vec,
  drug_p = "^G[0-9]{8}",
  sep_p = "[^0-9|^_]",
  batch_p = ".+"
)

Arguments

drug_vec

character vector with drug id(s)

drug_p

string with regex pattern for drug id. Set to Gnumber format by default: "G[0-9]{8}".

sep_p

string with regex pattern for separator. Set to any character except for digit and space

batch_p

string with regex pattern for batch substring. By default set to any character(s): ".+"

Value

charvec with Gnumber(s)

Details

By default, Gnumber(s) followed by any character (except for underscore and any digit) and any batch substring are cleaned:

  • G00060245.18 => G00060245

  • G00060245.1-8 => G00060245

  • G02948263.1-1.DMA => G02948263

  • Gnumber followed by the codrug

    • G03252046.1-2;G00376771 => G03252046

  • Gnumber followed by the two codrugs

    • G03256376.1-2;G00376771.1-19;G02557755 => G03256376

  • Gnumber followed by the drug name

    • G00018838, Cisplatin => G00018838

By default, Gnumber(s) followed by the "_" or digit (regardless the batch substring) are not cleaned:

  • Gnumber with suffix added to prevent duplicated ids

    • G00060245_(G00060245.1-8)

  • too long Gnumber

    • G123456789.1-12

Examples

remove_drug_batch("G00060245.18")
#> [1] "G00060245"
remove_drug_batch("G00060245.1-8")
#> [1] "G00060245"
remove_drug_batch("G00060245.1-1.DMA")
#> [1] "G00060245"

remove_drug_batch("G03252046.1-2;G00376771")
#> [1] "G03252046"
remove_drug_batch("G00018838, Cisplatin")
#> [1] "G00018838"
remove_drug_batch("G03256376.1-2;G00376771.1-19;G02557755")
#> [1] "G03256376"
remove_drug_batch("G00060245_(G00060245.1-8)")
#> [1] "G00060245_(G00060245.1-8)"
remove_drug_batch(c("G00060245.18", "G00060245.1-8", "G00060245.1-1.DMA"))
#> [1] "G00060245" "G00060245" "G00060245"

remove_drug_batch("DRUG_01.123", drug_p = "DRUG_[0-9]+")
#> [1] "DRUG_01"
remove_drug_batch("G00001234:22-1", sep_p = ":")
#> [1] "G00001234"
remove_drug_batch("G00001234.28", batch_p = "[0-9]+")
#> [1] "G00001234"