geneClass {INSPEcT} | R Documentation

## Retrieve the regulatory class for each gene

### Description

This method returns a factor that summarise the gene class (transcriptional regulatory mechanism) that INSPEcT has assigned to each gene. The classification depends on the chi-squared and Brown's method thresholds, that can be both provided as arguments. If the user decides a different thresholding respect to the default, these new values can be permanently set within the object.

### Usage

    geneClass(object, bTsh = NULL, cTsh = NULL)

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

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

    ## S4 method for signature 'INSPEcT_diffsteady'
    geneClass(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

### Value

A character containing the regulatory class for each gene

### See Also

`ratePvals`

### Examples

    nascentInspObj10 <- readRDS(system.file(package='INSPEcT', 'nascentInspObj10.rds'))
    geneClass(nascentInspObj10)
    # see the classification with another threshold for chi-squared test
    geneClass(nascentInspObj10, cTsh=.2)
    # set the new threshold permanently within the object
    modelSelection(nascentInspObj10)$thresholds$chisquare <- .2

[Package INSPEcT version 1.12.2 Index]