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

## Documentation for package ‘dnet’ version 1.0.9

- DESCRIPTION file.
- Package NEWS.

## Help Pages

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).
org.Hs.egHPPA | Annotations of Human Entrez Genes (EG) by Human Phenotype Phenotypic Abnormality (HPPA).
TCGA_mutations | TCGA mutational profiles across 12 major cancer types from Kandoth et al. (2013)
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