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Prediction Wrangler

int_prediction_wrangler.Rd

Internal function called by get_glm_scores. Not meant for out-of-package usage.

Usage

int_prediction_wrangler(
  these_predictions = NULL,
  these_samples_metadata = NULL,
  sample_id_col = NULL,
  row_to_col = FALSE,
  subtype_class = "5_class",
  categorical_factor = NULL,
  scale = NULL,
  bin_scores = FALSE,
  n_bins = 10,
  surv_time = NULL,
  surv_event = NULL,
  this_subtype = NULL,
  return_all = FALSE
)

Arguments

these_predictions

Required. Output from classify_samples().

these_samples_metadata

Required. Metadata associated with he prediction output. Also possible for the user to provide a metadata subset with samples of interest, the return will be restricted to the samples within the specified group.

sample_id_col

Optional parameter dictating the column name with sample IDs, the function expects this column to be sample_id but the user can override this if they know the name for this column.

row_to_col

Boolean parameter. Set to TRUE to transform row names of the metadata to a new column called sample_id. Default is FALSE.

subtype_class

Can be one of the following; 5_class or 7_class. Default is 5_class.

categorical_factor

Required parameter. This should be the categorical variable that is intended for testing. In addition, this should also be a variable of type factor, with exactly 2 levels.

scale

Optional parameter. A numeric value to scale the numeric scores. If provided, all numeric scores will be multiplied by this value.

bin_scores

Boolean parameter. Set to TRUE to bin the numeric scores into discrete bins. Default is FALSE.

n_bins

Optional parameter. The number of bins to use when binning numeric scores. Default is 10.

surv_time

Optional, should be the column name for the survival time (numeric) in the metadata.

surv_event

Optional, should be the column name for survival event (factor) in the metadata.

this_subtype

Optional parameter. Allows the user to subset the return to a specific subtype within the selected class. If not specified, the function will return a data frame based on all subtypes in the specified class.

return_all

Boolean parameter, set to TRUE to return all metadata columns. Default is FALSE.

Value

A data frame ready for get_glm, or get_survival.

Details

Takes an output from classify_samples() together with associated metadata and pre-processing it so that statistical tests can be executed on this data. For more info, see the documentation of get_glm_scores.

Examples

if (FALSE) { # \dontrun{
# No examples provided
} # }