Make biomarkers table

Make biomarkers table

Usage

make_biomarkers_table(
  data,
  biomarker_varnames = dplyr::pull(compile_biomarker_groups_table(), "biomarker"),
  biomarker_events_table,
  stratifying_var_names = "Gender"
)

Arguments

data

a data.frame() containing the columns specified by biomarker_varnames as well as stratifying_var_names

biomarker_varnames

a character vector matching a subset of the column names in data

biomarker_events_table

data.frame from construct_biomarker_events_table()

stratifying_var_names

a character vector specifying variables to stratify by

Value

a flextable::flextable()

Examples

biomarker_group_list <- list(
  "group 1" = c("Biomarker 1", "Biomarker 2"),
  "group 2" = c("Biomarker 3", "Biomarker 4"),
  "group 3" = "Biomarker 5"
)
biomarker_groups <- compile_biomarker_groups_table(
  dataset = sim_data,
  biomarker_group_list = biomarker_group_list
)

biomarker_varnames <-
  biomarker_groups |>
  dplyr::pull("biomarker")

biomarker_levels <-
  sim_data |>
  get_levels(biomarker_varnames)

biomarker_events_table <-
  construct_biomarker_events_table(
    biomarker_levels,
    biomarker_groups = biomarker_groups
  )

sim_data |> make_biomarkers_table(
  biomarker_events_table = biomarker_events_table,
  biomarker_varnames = biomarker_varnames,
  stratifying_var_names = "Sex"
)
#> # A tibble: 5 × 6
#>   category biomarker   levels     Male       Female     `p-value`
#> * <chr>    <chr>       <chr>      <formttbl> <formttbl>     <dbl>
#> 1 group 1  Biomarker 1 0, 1, 2    76.9%      75%            1    
#> 2 group 1  Biomarker 2 0, 1, 2    69.2%      83.3%          0.645
#> 3 group 2  Biomarker 3 0, 1       15.4%      25%            0.645
#> 4 group 2  Biomarker 4 0, 1, 2, 3 76.9%      75%            1    
#> 5 group 3  Biomarker 5 0, 1, 2, 3 76.9%      75%            1