export_risk_stratification_info {familiar} | R Documentation |
Extract and export cut-off values for risk group stratification.
Description
Extract and export cut-off values for risk group stratification by models in a familiarCollection.
Usage
export_risk_stratification_info(
object,
dir_path = NULL,
aggregate_results = TRUE,
export_collection = FALSE,
...
)
## S4 method for signature 'familiarCollection'
export_risk_stratification_info(
object,
dir_path = NULL,
aggregate_results = TRUE,
export_collection = FALSE,
...
)
## S4 method for signature 'ANY'
export_risk_stratification_info(
object,
dir_path = NULL,
aggregate_results = TRUE,
export_collection = FALSE,
...
)
Arguments
object |
A |
dir_path |
Path to folder where extracted data should be saved. |
aggregate_results |
Flag that signifies whether results should be aggregated for export. |
export_collection |
(optional) Exports the collection if TRUE. |
... |
Arguments passed on to
|
Details
Data is usually collected from a familiarCollection
object.
However, you can also provide one or more familiarData
objects, that will
be internally converted to a familiarCollection
object. It is also
possible to provide a familiarEnsemble
or one or more familiarModel
objects together with the data from which data is computed prior to export.
Paths to the previous files can also be provided.
All parameters aside from object
and dir_path
are only used if object
is not a familiarCollection
object, or a path to one.
Stratification cut-off values are determined when creating a model, using
one of several methods set by the stratification_method
parameter. These
values are then used to stratify samples in any new dataset. The available
methods are:
-
median
(default): The median predicted value in the development cohort is used to stratify the samples into two risk groups. -
fixed
: Samples are stratified based on the sample quantiles of the predicted values. These quantiles are defined using thestratification_threshold
parameter. -
optimised
: Use maximally selected rank statistics to determine the optimal threshold (Lausen and Schumacher, 1992; Hothorn et al., 2003) to stratify samples into two optimally separated risk groups.
Value
A data.table (if dir_path
is not provided), or nothing, as all data
is exported to csv
files.
References
Lausen, B. & Schumacher, M. Maximally Selected Rank Statistics. Biometrics 48, 73 (1992).
Hothorn, T. & Lausen, B. On the exact distribution of maximally selected rank statistics. Comput. Stat. Data Anal. 43, 121–137 (2003).