ratePvals: Retrieve a single p-value for each rate

Description

Retrieve a single p-value for each rate

This method is used to retrieve all the p-values combined with Brown's method that combines the results of the log likelihood ratio test results for all pairs tested for each rate and all genes. P-values will change according to the threshold set for the chi-squared test because it influences the model that will be taken into consideration to perform log likelihood ratio tests. To have a sense of the best parameter to choose, a sythetic data-set can be built and tested (makeSimModel, makeSimDataset) In case 'aic' has been selected via modelSelection method, this method assigns the chi-squared test result of the model selected by AIC to the respective variable rates

Usage

ratePvals(object, cTsh = NULL)
"ratePvals"(object, cTsh = NULL)
"ratePvals"(object, cTsh = NULL)

Arguments

object

An object of class INSPEcT or INSPEcT_model

cTsh

A numeric representing the threshold for the chi-squared test to consider a model as valid

Value

A matrix containing p-values calculated for each rate

Details

ratePvlas retrieve a single p-value for each rate thanks to multiple log likelihood tests performed on nested models that has a chi-squared test below the selected threshold. Among the many p-values that log likelihood ratio test calculate, a single p-value is obtaied applying Brown's method for combining dependent p-values.

Examples

Run this code

data('mycerIds10', package='INSPEcT')
ratePvals(mycerIds10)
# calculate agin the p-values with Brown with a different threshold 
# for considering a model valid for the log likelihood ratio test
ratePvals(mycerIds10, cTsh=.2)
# Set permaenently the chi-squared threshold at .2 for mycerIds10 object
thresholds(mycerIds10)$chisquare <- .2