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 (
In case 'aic' has been selected via
this method assigns the chi-squared test result of the model selected by AIC
to the respective variable rates
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An object of class INSPEcT or INSPEcT_model
A numeric representing the threshold for the chi-squared test to consider a model as valid
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.
A matrix containing p-values calculated for each rate
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data('nascentInspObj10', package='INSPEcT') 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 thresholds(nascentInspObj10)$chisquare <- .2
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