Compute H-Score based on parameters in a score data file

Compute H-Score based on parameters in a score data file

compute_h_score_from_score_data(
  csd,
  score_path,
  tissue_categories = NULL,
  .by = "Slide ID",
  phenotype = NULL
)

Arguments

csd

Cell seg data to use.

score_path

Path to to a score_data file (may be merged or not).

tissue_categories

optionally specify tissue categories of interest. If not given, tissue categories are taken from the score file.

.by

Column to aggregate by

phenotype

Optional phenotype to subset csd.

Value

A data frame with one row per Slide ID, showing cell counts and percents in each bin and the H-Score. See compute_h_score.

See also

Other aggregation functions: compute_density_from_cell_summary(), compute_density_from_table(), compute_h_score(), compute_mean_expression_many(), compute_mean_expression(), compute_positivity_many(), compute_positivity(), count_phenotypes(), counts_to_percents()