geneClass {INSPEcT} | R Documentation |
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.
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)
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 |
cTsh |
A numeric representing the threshold for the chi-squared test to consider a model as valid |
A character containing the regulatory class for each gene
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