ratePvals {INSPEcT} | R Documentation

## Retrieve a single p-value for each rate

### Description

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, bTsh = NULL, cTsh = NULL)

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

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

### Arguments

`object` | An object of class INSPEcT or INSPEcT_model
`bTsh` | A numeric representing the p-value threshold for considering a rate as variable. P-values are calculated through `ratePvals`
`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

    nascentInspObj10 <- readRDS(system.file(package='INSPEcT', 'nascentInspObj10.rds'))
    ratePvals(nascentInspObj10)
    # calculate agin the p-values with Brown with a different threshold
    # for considering a model valid for the log likelihood ratio test
    ratePvals(nascentInspObj10, cTsh=.2)
    # Set permaenently the chi-squared threshold at .2 for nascentInspObj10 object
    modelSelection(nascentInspObj10)$thresholds$chisquare <- .2

[Package INSPEcT version 1.12.2 Index]