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Assess MMR status based on IHC biomarker scores

Source: R/post_consolidation.R
assess_mmr_status.Rd

Assess MMR status based on IHC biomarker scores

Usage

assess_mmr_status(biomarkers_data)

Arguments

biomarkers_data

data frame with biomarker scores, which must include the following columns: "mlh1", "msh2", "msh6", "pms2". The function will add a new column "mmr_ihc_4" with the MMR status based on the following rules:

  • If at least one of MSH6, PMS2, MLH1, MSH2 is absent, MMR status is 'deficient'.

  • If at least one of MSH6, PMS2 is unknown (i.e., "Unk"), MMR status is 'Unk'.

  • If all of MSH6, PMS2 are present and none of MSH6, PMS2, MLH1, MSH2 is absent, MMR status is 'intact'.

Value

A data frame with an additional column "mmr_ihc_4" containing the MMR status ("deficient", "intact", or "Unk") for each row.

Examples

library(TMAtools)
# create example biomarker data
example_data <- data.frame(
  mlh1 = c("present", "absent", "present"),
  msh2 = c("present", "present", "present"),
  msh6 = c("present", "present", "Unk"),
  pms2 = c("present", "present", "present"),
  stringsAsFactors = FALSE
)
assess_mmr_status(example_data)
#>      mlh1    msh2    msh6    pms2 mmr_ihc_4
#> 1 present present present present    intact
#> 2  absent present present present deficient
#> 3 present present     Unk present       Unk