Function reference • FBNNet

All functions
`BoolNet_CellCycle_Network`	BoolNet CellCycle Network
`buildProbabilityTreeOnTargetGene()`	build Probability Tree On the targetGene
`checkNumeric()`	A simple function to check a value is numeric or not
`checkProbabilityTypeData()`	A simple function to check a value is probability type data.
`CheckRightTypeTimeseriesData()`	This function is used to check whether or not the data is the right type for `FBNNet`.
`checkSimilarity()`	Check the similarity between time series
`Common_Genes_Clusters`	Fundamental Boolean model Example
`Common_Genes_Leukeamia`	Fundamental Boolean model Example
`constructFBNCube()`	Create an Orchard cube
`constructFBNFunctions()`	An internal function to construct the FBN functions with an expression tree.
`convertInteraction()`	A function to convert the traditional network interactions to fundamental Boolean network interactions.
`convertIntoExpressionTree()`	An internal function to convert a splitted Boolean expression into an expression tree.
`convertIntoSampleTimeSeries()`	This method is used to converts normalized timeseries data into a list of samples
`convertMinedResultToFBNNetwork()`	An internal function to convert the mined result to FBN network
`convertTimeseriesProbsetNameToGeneName()`	A method that map the row names (probesets) of a specific timeseries data into gene names Old function name mapPropersetsWithhgu133plus2Db
`convertToBooleanNetworkCollection()`	A function to convert the traditional Boolean network to fundamental Boolean network collection.
`convertToFBNNetwork()`	Convert a boolean network object to fundamental boolean function object
`ConvertToNetworkGraphicObject()`	Convert To Network Graphic Object
`convert_to_NGO()`	Convert To Dynamic Network Graphic Object
`DAVID_Gene_List`	DAVID Gene Annotation data
`dissolve()`	A function moves the sub list items to its parent list
`dividedVectorIntoSmallgroups()`	An internal function that divides large data into small groups.
`doNonParallelWork()`	Executing a list of processes not in parallel
`doNonParallelWorkDecrease()`	Executing a list of processes in parallel with decreasing list
`doParallelWork()`	Executing a list of processes in parallel
`DrawingAttractorInternal()`	An Internal method to draw attractor internally
`ExampleNetwork`	Example Network data
`ExampleTimeseriesData`	Fundamental Boolean model Example
`extractGeneStateFromTimeSeriesCube()`	A function that extract gene states from time series cube
`FBNBioinformatics`	Functions related to Bioinformatics
`FBNcellcycleNetwork`	Fundamental Boolean model Cell Cycle
`FBNDataReduction()`	Remove duplicate timeseries sample data
`FBNExampleNetworks`	Example Network data
`FBNNetwork.Graph.DrawAttractor()`	A method to draw attractors in the form of dynamic Network
`FBNNetwork.Graph()`	Executing a list of processes in parallel with decreasing list
`filterNetworkConnections()`	filtering out non regulate genes
`filterNetworkConnectionsByGenes()`	Find Backward Network By Genes
`filterNetworkConnectionsByInputGenes()`	Find Backward Network By Genes
`findAllBackwardRelatedGenes()`	Find Backward Network By Genes
`findAllForwardRelatedGenes()`	Find Forward related Network By Genes internal
`findAllInputGenes()`	An internal function to find all input genes from a group of genes
`findAllTargetGenes()`	An internal function to find all target genes from a group of network interactions
`findBackwardRelatedNetworkByGenes()`	Find Backward Network By Genes
`findForwardRelatedNetworkByGenes()`	Find Forward related Network By Genes
`flatDeMorganLaw()`	An internal function to flat a splitted Boolean expression with DeMorganLaw
`generateAllCombinationBinary()`	Generate all combination of binary data based on an vector of genes
`GenerateDynamicNetworkGraphicObject()`	An Internal method to generate dynamic network graphic objects
`generateFBMNetwork()`	Generate Fundamental Boolean Model type of Network
`generateFBNInteraction()`	generate FBN interaction
`generateSimilarReport()`	Generate similarity report
`generateSimilaryReport()`	This method compare two timeseries data and generate similar report
`genereateBoolNetTimeseries()`	A method to generate BoolNet type of timeseries data for generating BoolNet type of testing timeseries data
`getFBMSuccessor()`	This method is used to calculate the next state
`getGenePrababilities()`	The main function to main FBN probabilities from time series data
`getGenePrababilities_advanced()`	The main function to main FBN probabilities from time series data
`getGenePrababilities_basic()`	A function to get gene probabilities
`getGenePrababilities_measurements()`	Get the main measurements based on the input data
`getncbiseq()`	Retrieving genome sequence data using SeqinR. The code is a sample from the book 'a little book of r for bioinformatic'
`getProbabilityFromFunctionInput()`	An internal method to get the probability of regulatory function from the cube
`getRelatedGeneTimeseries()`	A function to reduce the timeseries data based on the gene list
`getSpecificExpressedGenes()`	getSpecificExpressedGenes
`identifyDifferentiallyExpressedGenes()`	A benchmark type function to test a complete process of FBN model All sub time series must contain the same number of timepoints Step 3, identify significantly expressed genes, which are strongly related with the samples / study purposes
`isAppliedDeMorganLaw()`	An internal function to check a splitted Boolean expression is applied DeMorganLaw
`isAtomNode()`	An internal function to check if an expression is atomic node
`isBooleanTypeTimeseriesData()`	A simple function to check a value is boolean type data.
`isSatisfied()`	Is the Gene State Satisfied
`isSubExpression()`	An internal function to check if an expression is a sub expression
`Leukeamia_Networks`	Fundamental Boolean model Example
`Leukeamia_Timeseries`	Fundamental Boolean model Example
`loadFBNNetwork()`	Load FBN network data into a FBN network object
`mapProbesetNames()`	This method is used to map probeset names with gene names
`mapToGeneNameWithhgu133plus2Db()`	Annotation method
`mergeClusterNetworks()`	A function to merge the networks from clustered FBN cube.
`mergeInteraction()`	A function to merge the network interactions
`mergeNetwork()`	A function to merge tow networks.
`mineFBNNetwork()`	Mine FBN Networks from an Orchard cube
`mineFBNNetworkStage2()`	Internal method
`mineFBNNetworkWithCores()`	An internal function
`networkFiltering()`	A function to filter networks.
`networkFixUpdate()`	A method to fix a specific genes in the FBM networks
`output_annotated_genes()`	A method to convert a vector of gene names to annotated gene details
`output_genes()`	A method to output a vector of gene names separated by comma
`output_timesereis_based_on_genes()`	A method to reorder a matrix by a vector
`plotNetwork()`	A function to plot the Fundamental boolean networks
`print(<FBMAttractors>)`	A S3 method to print the FBM attractors
`print(<FundamentalBooleanNetwork>)`	A S3 method to print the FBM network
`process_cube_algorithm()`	Get the main measurements based on the input data
`randomGenerateBinary()`	A method to generate binary data randomly
`randomSelection()`	A random selection function denoted as P[]
`rbind_all_columns()`	A method to bind two matrix by row
`reconstructTimeseries()`	This method is used to reconstruct time series data
`regenerateInteractions()`	An internal function to reconstrunct FBN functions
`removeDuplicates()`	Internal method
`removeFistLevelBracket()`	An internal function to remove the first brasket
`reorderSampleTimeSeries()`	This method is used to sort time series order based on columns
`rep_col()`	A method to duplicate a column
`rep_row()`	A method to duplicate a row
`searchForAttractors()`	A function to find all possible FBM (Fundamental Boolean models) attractors
`search_FBN_core()`	Internal method
`similarityBetweenMatrix()`	This function is used to compare the similarity of two matrixes
`splitExpression()`	A function to split an expression into a vector of input
`StaticNetwork()`	Display a static network in a slice
`StaticNetworkInSlice()`	Display a dynamic network in a slice
`transitionStates()`	A function do the state transition
`yeastTimeSeries`	Yeast Timeseries Data

Reference

All functions