getResultsDf: Obtain results stored in data.frames

In kueckelj/SPATA2: A Toolbox for Spatial Gene Expression Analysis

Obtain results stored in data.frames

Description

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.

Usage

getResultsDf(object, ...)

## S4 method for signature '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 signature '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.

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.

Value

Data.frame.

kueckelj/SPATA2 documentation built on March 16, 2024, 10:25 a.m.