Obtain results stored in data.frames

Extracts content of slot @results of screening S4 objects. For a more detailed explanation of what the slot contains check the description of the respective S4 class. E.g. with ?SpatialTrajectoryScreening.

getResultsDf(object, ...)

# S4 method for ImageAnnotationScreening
getResultsDf(
  object,
  eval = "ias_score",
  pval = "p_value_mean_adjusted",
  arrange_by = eval,
  threshold_eval = 0,
  threshold_pval = 1,
  model_subset = NULL,
  model_remove = NULL,
  best_only = FALSE
)

# S4 method for SpatialTrajectoryScreening
getResultsDf(
  object,
  eval = "sts_score",
  pval = "p_value",
  arrange_by = eval,
  threshold_eval = 0,
  threshold_pval = 1,
  model_subset = NULL,
  model_remove = NULL,
  best_only = FALSE
)

Arguments

object

Any object for which a method has been defined.

Value

Data.frame.

Details

Without any argument specification the function getResultsDf() returns the complete data.frame. The arguments can be used to filter the results. Filtering works as follows:

1. Model-fits are filtered according to the input of model_subset and model_remove.

2. Model-fits are filtered according to the threshold_ arguments.

3. If best_only is set to TRUE, model-fits are filtered such that the best model-fit (among the remaining models from 1.) for every gene remains. E.g. if gene GFAP fits to model linear_descending with a score of 0.9 and to immediate_descending with a score of 0.75 the model-fit GFAP-linear_descending remains in the output.

The output is arranged by the evaluation.