INSPEcT (version 1.2.2)

geneClass: Retrieve the regulatory class for each gene

Description

Retrieve the regulatory class for each gene

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

data('mycerIds10', package='INSPEcT')
geneClass(mycerIds10)
# see the classification with another threshold for chi-squared test 
geneClass(mycerIds10, cTsh=.2)
# set the new threshold permanently within the object
thresholds(mycerIds10)$chisquare <- .2