CalcAdj: Calculate the adjacency matrix
In uc-bd2k/paslincs: Pathway activity signatures from LINCS L1000 consensus gene signatures
Description
Usage
Arguments
Value
Examples
Description
Calculate the adjacency matrix of the signed undirected graph of the pathway topology
Usage
1
CalcAdj(EdgeFrom,EdgeTo,interaction)
Arguments
EdgeFrom
A character vector of gene symbols of one end of the edges.
EdgeTo
A character vector of gene symbols of the other end of the edges.
interaction
A numeric vector with components of 1 and -1 to denote activation and inhibition for the edges.
Value
If the graph of the pathway topology is balanced (no conflict in the interactions), then a numeric adjacency matrix is returned. The row names and column names are the nodes in the pathway.
Examples
1
2
3
4
5
# obtain edge information of a pathway
Edges <- AllEdges[AllEdges$Pathway=="hsa04150",]
# calculate the signed adjacency matrix of the pathway topology
CalcAdj(EdgeFrom=Edges$GeneSymbol_a,EdgeTo=Edges$GeneSymbol_b,interaction=Edges$Interaction)
uc-bd2k/paslincs documentation built on May 28, 2020, 8:20 a.m.
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Description Usage Arguments Value Examples
Description
Calculate the adjacency matrix of the signed undirected graph of the pathway topology
Usage
1 | CalcAdj(EdgeFrom,EdgeTo,interaction)
|
Arguments
EdgeFrom |
A character vector of gene symbols of one end of the edges. |
EdgeTo |
A character vector of gene symbols of the other end of the edges. |
interaction |
A numeric vector with components of 1 and -1 to denote activation and inhibition for the edges. |
Value
If the graph of the pathway topology is balanced (no conflict in the interactions), then a numeric adjacency matrix is returned. The row names and column names are the nodes in the pathway.
Examples
1 2 3 4 5 | # obtain edge information of a pathway
Edges <- AllEdges[AllEdges$Pathway=="hsa04150",]
# calculate the signed adjacency matrix of the pathway topology
CalcAdj(EdgeFrom=Edges$GeneSymbol_a,EdgeTo=Edges$GeneSymbol_b,interaction=Edges$Interaction)
|
R Package Documentation
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We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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