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]