R/AllGenerics.R

In ste-depo/INSPEcT: Modeling RNA synthesis, processing and degradation with RNA-seq data

####################################
# generics for class INSPEcT_model ####
####################################

#' Visualize criteria used for rate variability
setGeneric('modelSelection', function(object) 
	standardGeneric('modelSelection'))
#' Retrieve all results of chi-squared test
setGeneric('chisqtest', function(object, ...) 
	standardGeneric('chisqtest'))
#' Retrieve results of chi-squared test for the selected models
setGeneric('chisqmodel', function(object, gc=NULL, tpts=NULL, ...) 
	standardGeneric('chisqmodel'))
#' Retrieve results of log likelihood test
setGeneric('logLik', function(object, ...) 
	standardGeneric('logLik'))
#' Retrieve a single p-value for each rate
setGeneric('ratePvals', function(object) 
	standardGeneric('ratePvals'))
#' Calculate a single p-value for each rate
setGeneric('calculateRatePvals', function(object, modelSelection = c('aic','llr','hib'), preferPValue = TRUE, padj = TRUE, 
																					p_goodness_of_fit = .1, p_variability=rep(.05,3), limitModelComplexity = FALSE) 
	standardGeneric('calculateRatePvals'))
#' Retrieve the regulatory class for each gene
setGeneric('geneClass', function(object, ...)
	standardGeneric('geneClass'))
#' Calculate modeled rates and concentrations
setGeneric('makeModelRates', function(object, ...) 
	standardGeneric('makeModelRates'))
#' Compute confidence intervals
setGeneric('computeConfidenceIntervals', function(object, BPPARAM=SerialParam()) 
	standardGeneric('computeConfidenceIntervals'))
#' Set confidence intervals
setGeneric('setConfidenceIntervals', function(object, confidenceIntervals) 
	standardGeneric('setConfidenceIntervals'))
#' Generate synthetic rates and concentrations
setGeneric('makeSimDataset', function(object, tpts, nRep, NoNascent = FALSE, seed=NULL, b = 0.3, tL = 1/6, noise_sd = 4.0)
	standardGeneric('makeSimDataset'))
#' Display rate classification performance
setGeneric('correlationPlot', function(object, object2, plot=TRUE) 
	standardGeneric('correlationPlot'))
#' Display rate classification performance
setGeneric('rocCurve', function(object, object2, plot=TRUE, comparative=FALSE) 
	standardGeneric('rocCurve'))
#' Display rate classification performance with thresholds visible at x-axis
setGeneric('rocThresholds', function(object, object2, xlim=c(1e-5,1), plot=TRUE) 
	standardGeneric('rocThresholds'))

#############################
# generics for class INSPEcT ####
###############################

#' Accessor to the slot tpts of an INSPEcT object
setGeneric('tpts', function(object) 
	standardGeneric('tpts'))
#' Accessor to the slot labeledSF of an INSPEcT object
setGeneric('labeledSF', function(object) 
	standardGeneric('labeledSF'))
#' remove modelling information from INSPEcT object
setGeneric('removeModel', function(object) 
	standardGeneric('removeModel'))
#' Get the number of genes within the INSPEcT object
setGeneric('nGenes', function(object) 
	standardGeneric('nGenes'))
#' Get the number of time points within the INSPEcT object
setGeneric('nTpts', function(object) 
	standardGeneric('nTpts'))
#' Get and set number parameters for the modeling
setGeneric('modelingParams', function(object) 
	standardGeneric('modelingParams'))
#' Retrieve pre-modeling rates and concentrations
setGeneric('ratesFirstGuess', function(object, feature) 
	standardGeneric('ratesFirstGuess'))
#' Retrieve pre-modeling rates and concentrations variance
setGeneric('ratesFirstGuessVar', function(object, feature) 
	standardGeneric('ratesFirstGuessVar'))
#' @title Launch the modeling process
#' @description Launch the modeling process with parameters set with \code{\link{modelingParams}}
setGeneric('modelRates', function(object, estimateRatesWith = c('der', 'int'), useSigmoidFun = TRUE, 
																	nInit = 10, nIter = 300, Dmin = 1e-06, Dmax = 10, 
																	seed=NULL, BPPARAM=SerialParam())
	standardGeneric('modelRates'))
#' Launch the modeling process without imposing sigmoid/impulse functional form
setGeneric('modelRatesNF', function(object, BPPARAM=SerialParam()) 
	standardGeneric('modelRatesNF'))
#' Build the synthetic rates shaped on a dataset
setGeneric('makeSimModel', function(object, nGenes, newTpts=NULL
		, probs=c(constant=.5,sigmoid=.3,impulse=.2), na.rm=TRUE, seed=NULL) 
	standardGeneric('makeSimModel'))
#' Build the synthetic rates with oscillatory pattern
setGeneric('makeOscillatorySimModel', function(object, nGenes
		, oscillatoryk3=FALSE, k3delay=NULL, na.rm=TRUE, seed=NULL) 
	standardGeneric('makeOscillatorySimModel'))
#' Retrieve the modeled rates and concentrations
setGeneric('viewModelRates', function(object, feature) 
	standardGeneric('viewModelRates'))
#' Retrieve the modeled Confidence Intervals
setGeneric('viewConfidenceIntervals', function(object, feature) 
	standardGeneric('viewConfidenceIntervals'))
#' Plot the pre-modeled and modeled profiles for one gene
setGeneric('plotGene', function(object, ix, relative_expression=FALSE, 
                                fix.yaxis=FALSE, priors=TRUE, constantModel=FALSE) 
	standardGeneric('plotGene'))
#' Heatmap that represent the fold changes of all the five features
setGeneric('inHeatmap', function(object, type='pre-model'
	, breaks=seq(-1,1,length.out=51)
	, palette=colorRampPalette(c("green", "black", "firebrick3"))
	, plot_matureRNA=FALSE, absoluteExpression=TRUE
	, show_rowLabels=TRUE, clustering=TRUE, clustIdx=3:5)
	standardGeneric('inHeatmap'))
#' Generate an object of class INSPEcT_diffsteady from an object of class INSPEcT
setGeneric('compareSteady', function(inspectIds, BPPARAM=SerialParam()) 
	standardGeneric('compareSteady'))
#' Classify genes as delayed by the processing using the delta and tau metrics
setGeneric('processingDelay', function(inspectIds, tauThreshold=1.2,deltaThreshold=1.0, silent=TRUE) 
	standardGeneric('processingDelay'))
#' @rdname processingDelay
setGeneric('calculateDelta', function(inspectIds, silent=FALSE) 
	standardGeneric('calculateDelta'))
#' @rdname processingDelay
setGeneric('calculateTau', function(inspectIds, silent=FALSE) 
	standardGeneric('calculateTau'))
#' Retrieve the convergence for the selected models of each gene
setGeneric('convergence', function(object) 
	standardGeneric('convergence'))

##########################################
# generics for class INSPEcT_diffsteady ####
##########################################

#' @rdname INSPEcT_diffsteady-class
setGeneric('synthesis', function(object) standardGeneric('synthesis'))
#' @rdname INSPEcT_diffsteady-class
setGeneric('processing', function(object) standardGeneric('processing'))
#' @rdname INSPEcT_diffsteady-class
setGeneric('degradation', function(object) standardGeneric('degradation'))

###############################################
# generics for class INSPEcT_steadyNoNascent ####
###############################################

#' Get premature RNA expressions from an object of class INSPEcT_diffsteady
setGeneric('premature', function(object) 
	standardGeneric('premature'))
#' Get mature RNA expressions from an object of class INSPEcT_diffsteady
setGeneric('mature', function(object) 
	standardGeneric('mature'))

#' Calculate post-transcriptional ratio from an object of class INSPEcT_diffsteady
setGeneric('PTratio', function(object, infToNA=TRUE) 
	standardGeneric('PTratio'))

#' Get premature RNA expressions variances from an object of class INSPEcT_diffsteady
setGeneric('prematureVar', function(object) 
	standardGeneric('prematureVar'))
#' Get mature RNA expressions variances from an object of class INSPEcT_diffsteady
setGeneric('matureVar', function(object) 
	standardGeneric('matureVar'))

#' Identify post-transcriptionally regulated genes from an object of class INSPEcT_diffsteady
setGeneric('compareSteadyNoNascent', function(inspectIds,
														 expressionThreshold=0.25, log2FCThreshold=2., trivialAngle=NaN, 
														 returnNormScores=FALSE, referenceCondition='median') 
	standardGeneric('compareSteadyNoNascent'))

#' Calculate the post-transcriptional ratio from an object of class INSPEcT_diffsteady
setGeneric('PTreg', function(object) 
	standardGeneric('PTreg'))

#' Plot the premature/mature trend from an object of class INSPEcT_diffsteady
setGeneric('plotPMtrend', function(inspectIds) 
	standardGeneric('plotPMtrend'))

#' Plot the premature/mature expression of a gene and the global trend from an object of class INSPEcT_diffsteady
setGeneric('plotPMgene', function(object, gene_id, samples_colors=1) 
	standardGeneric('plotPMgene'))