scoreData: Predicting new regulatory regions

In LedPred: Learning from DNA to Predict Enhancers

Description

scoreData function predict new regulatory regions using SVM model from a test data set

Usage

scoreData(data, ledpred = NULL, model = NULL, score.file = NULL)

Arguments

data	data.frame containing the test set. This test set must have the same descriptive features as the one that were used to build the model.
ledpred	Returned object from the LedPred function
model	Returned object of the createModel function
score.file	A character string that will be used as the file name for the output file, if it is NULL (default), no file is writen. The output file takes the form of two columns with object names and scores.

Value

A 2-columns dataframe. First column containg the SVM model prediction probabilities and the second containing the corresponding regions

Examples

data(crm.features)
data(svm.model)
#pred.test <- scoreData(data.granges=crm.features, model=svm.model,
# score.file="test_prediction.tab")

LedPred documentation built on Nov. 8, 2020, 8 p.m.