Skip to contents

Consolidate biomarker scores

Source: R/translate_and_consolidate.R
translate_and_consolidate_scores.Rd

This function translates numerical scores of biomarkers to nominal scores and consolidates them for each case.

Usage

translate_and_consolidate_scores(
  biomarkers_file,
  required_biomarkers = NULL,
  get_dict = NULL,
  output_file = NULL
)

Arguments

biomarkers_file

Path to the Excel file containing biomarker data.

required_biomarkers

A vector of required biomarkers. If NULL, default biomarkers are used.

get_dict

A function that returns a dictionary for translating numerical scores to nominal scores. If NULL, a default function is used.

output_file

Optional path to the output file. If NULL, the function will not save the output.

Value

A data frame with consolidated biomarker scores and MMR status.

See also

get_default_dict for the default dictionary function.

Examples

library(TMAtools)
# grab folder with example TMA datasets
tma_dir <- system.file("extdata", "tma1", package = "TMAtools")
# define output files
combined_tma_file <- "combined_tma.xlsx"
deconvoluted_tma_file <- "deconvoluted_tma.xlsx"
consolidated_tma_file <- "consolidated_tma.xlsx"

# combine TMA datasets
combine_tma_spreadsheets(
 tma_dir = tma_dir,
 output_file = combined_tma_file
)
#> Using TMA map from the file: /home/runner/work/_temp/Library/TMAtools/extdata/tma1/example_er.xlsx

# deconvolute combined TMA dataset
deconvolute(
   tma_file = combined_tma_file,
   output_file = deconvoluted_tma_file
)

# translate numerical biomarker scores to nominal scores
# and consolidate them for each case
consolidated_data <- translate_and_consolidate_scores(
  biomarkers_file = deconvoluted_tma_file,
  required_biomarkers = c("ER", "TP53")
)
#> Consolidating ER using columns: ER.c1, ER.c2
#> Consolidating TP53 using columns: TP53.c1, TP53.c2
head(consolidated_data)
#> # A tibble: 6 × 7
#>   core_id ER.c1          ER.c2          er             TP53.c1     TP53.c2          tp53   
#>   <chr>   <chr>          <chr>          <chr>          <chr>       <chr>            <chr>  
#> 1 1       Unk            Unk            Unk            cytoplasmic complete absence mutated
#> 2 5       diffuse (>50%) diffuse (>50%) diffuse (>50%) Unk         subclonal        mutated
#> 3 9       Unk            Unk            Unk            cytoplasmic subclonal        mutated
#> 4 11      Unk            Unk            Unk            subclonal   wild type        mutated
#> 5 2       Unk            focal (1-50%)  focal (1-50%)  subclonal   Unk              mutated
#> 6 6       Unk            focal (1-50%)  focal (1-50%)  Unk         Unk              Unk