Integrative Analysis of Omics Data in Terms of Network, Evolution and Ontology

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Documentation for package ‘dnet’ version 1.1.7

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dBUMfit Function to fit a p-value distribution under beta-uniform mixture model
dBUMscore Function to transform p-values into scores according to the fitted beta-uniform mixture model and/or after controlling false discovery rate
dCheckParallel Function to check whether parallel computing should be used and how
dCommSignif Function to test the significance of communities within a graph
dContrast Function to help build the contrast matrix
dDAGancestor Function to find common ancestors of two terms/nodes from a direct acyclic graph (DAG)
dDAGannotate Function to generate a subgraph of a direct acyclic graph (DAG) induced by the input annotation data
dDAGgeneSim Function to calculate pair-wise semantic similarity between genes based on a direct acyclic graph (DAG) with annotated data
dDAGinduce Function to generate a subgraph of a direct acyclic graph (DAG) induced by given vertices
dDAGlevel Function to define/calculate the level of nodes in a direct acyclic graph (DAG)
dDAGreverse Function to reverse the edge direction of a direct acyclic graph (DAG)
dDAGroot Function to find the root node of a direct acyclic graph (DAG)
dDAGtermSim Function to calculate pair-wise semantic similarity between input terms based on a direct acyclic graph (DAG) with annotated data
dDAGtip Function to find the tip node(s) of a direct acyclic graph (DAG)
dEnricher Function to conduct enrichment analysis given the input data and the ontology in query
dEnricherView Function to view enrichment results of dEnricher
dFDRscore Function to transform fdr into scores according to log-likelihood ratio between the true positives and the false positivies and/or after controlling false discovery rate
dFunArgs Function to assign (and evaluate) arguments with default values for an input function
dGSEA Function to conduct gene set enrichment analysis given the input data and the ontology in query
dGSEAview Function to view enrichment results in a sample-specific manner
dGSEAwrite Function to write out enrichment results
dNetConfidence Function to append the confidence information from the source graphs into the target graph
dNetFind Function to find heuristically maximum scoring subgraph
dNetInduce Function to generate a subgraph induced by given vertices and their k nearest neighbors
dNetPipeline Function to setup the pipeline for finding maximum-scoring subgraph from an input graph and the signficance imposed on its nodes
dNetReorder Function to reorder the multiple graph colorings within a sheet-shape rectangle grid
dPvalAggregate Function to aggregate p values
dRDataLoader Function to load dnet built-in RData
dRWR Function to implement Random Walk with Restart (RWR) on the input graph
dRWRcontact Function to estimate RWR-based contact strength between samples from an input gene-sample data matrix, an input graph and its pre-computed affinity matrix
dRWRpipeline Function to setup a pipeine to estimate RWR-based contact strength between samples from an input gene-sample data matrix and an input graph
dSVDsignif Function to obtain SVD-based gene significance from the input gene-sample matrix
ig.HPPA Human Phenotype Phenotypic Abnormality (HPPA).
ig.HPPA Human Phenotype Phenotypic Abnormality (HPPA).
visBoxplotAdv Function to visualise a data frame using advanced boxplot
visDAG Function to visualise a direct acyclic graph (DAG) with node colorings according to a named input data vector (if provided)
visGSEA Function to visualise running enrichment score for a given sample and a gene set
visNet Function to visualise a graph object of class "igraph" or "graphNEL"
visNetAnimate Function to animate the same graph but with multiple graph node colorings according to input data matrix
visNetArc Function to visualise an igraph object via arc diagram
visNetCircle Function to visualise an igraph object via circle diagram
visNetMul Function to visualise the same graph but with multiple graph node colorings according to input data matrix
visNetReorder Function to visualise the multiple graph colorings reorded within a sheet-shape rectangle grid