ratePvals {INSPEcT} | R Documentation

## 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)

    ## S4 method for signature 'INSPEcT_model'
    ratePvals(object, cTsh = NULL)

    ## S4 method for signature 'INSPEcT'
    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

### 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.

### Value

A matrix containing p-values calculated for each rate

### See Also

`makeSimModel`, `makeSimDataset`

### Examples

    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

[Package INSPEcT version 1.10.0 Index]