The function coerces an adjacency matrix to a Pathway. Two types of matrices are allowed. The first one, where 1 denotes an edge between two nodes and 0 otherwise. This matrix is coerced into a simply pathway were type of all edges is set to "process". The second type of adjacency matrix contains: 1 for an activation, -1 for an inhibition and 0 otherwise (=no edge between two nodes). In this case, activations are set to "process(activation)" and inhibition to "process(inhibition)". The symetricity of the matrix is used to decide between directed and undirected graph. Symmetric matrix is expected for undirected graph and only the lower triangle of the matrix is used to extract the edges of the graph.
● Data Source:
BioConductor
● Keywords: manip
● Alias: AdjacencyMatrix2Pathway
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clipper is a method for topological gene set analysis. It implements a two-step empirical approach based on the exploitation of graph decomposition into a junction tree to reconstruct the most relevant signal path. In the first step clipper selects significant pathways according to statistical tests on the means and the concentration matrices of the graphs derived from pathway topologies. Then, it "clips" the whole pathway identifying the signal paths having the greatest association with a specific phenotype.
● Data Source:
BioConductor
● Keywords: htest
● Alias: clipper
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DEGraph implements recent hypothesis testing methods which directly assess whether a particular gene network is differentially expressed between two conditions. In employs Graph Laplacian, Fourier transformation and multivariate T2-statistic
● Data Source:
BioConductor
● Keywords: htest
● Alias: DEGraph
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ToPASeq-deprecated
(Package: ToPASeq) :
Deprecated functions in package sQuote{ToPASeq
These functions are provided for compatibility with older versions of ‘ToPASeq’ only, and will be defunct at the next release.
● Data Source:
BioConductor
● Keywords:
● Alias: AdjacencyMatrix2pathway, KEGG2pathway, ToPASeq-deprecated, graphNEL2pathway
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The function parses a KGML file from KEGG into a Pathway.
● Data Source:
BioConductor
● Keywords: manip
● Alias: KEGG2Pathway
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A function runs PRS method on a gene expression data matrix or count matrix and vector dividing samples into two groups and a set of pathways from graphite package. The PRS method (please see Reference for the details) was adapted to graphite's graphs where each node is represented only by one gene.
● Data Source:
BioConductor
● Keywords: htest
● Alias: PRS
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The function runs PWEA method (please see References for the details) on gene expression data matrix, vector specifing to which group a sample belongs and a list of pathway graphs. Briefly, it is a weighted GSEA-like method. The weightes are based on the distance and Pearson's correlation between genes in a pathway.
● Data Source:
BioConductor
● Keywords: htest
● Alias: PWEA
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The function runs SPIA method on microarray or RNA-Seq data. The implementatio includes the identification of differentially expressed genes and transformation of pathways' topologies to an appropriate form. The SPIA method combines two independent p-values. One p-value comes from overrepresentation analysis and the other is so called pertubation factor.
● Data Source:
BioConductor
● Keywords: htest
● Alias: SPIA
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The functions analyses the differential expression of pathways via TAPPA method. Expression is compared between two groups of samples by Mann-Whitney test. P-values are later adjusted for multiple hypothesis testing by Benjamini-Hochberg's FDR method.
● Data Source:
BioConductor
● Keywords: htest
● Alias: TAPPA
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The package implementats several methods for topology-based pathway analysis of microarray data. The methods present in here are: SPIA, TopologyGSA, DEGraph, Clipper, PWEA, TAPPA, TBS. SPIA, PWEA and TBS were also adapted for RNASeq data.
● Data Source:
BioConductor
● Keywords: package
● Alias: ToPASeq, ToPASeq-package
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