Description Usage Arguments Value Examples

Calculate consistency score

1 |

`EdgeFrom` |
A character vector of gene symbols of one end of the edges. This parameter is ignored if |

`EdgeTo` |
A character vector of gene symbols of the other end of the edges. This parameter is ignored if |

`interaction` |
A numeric vector with components of 1 and -1 to denote activation and inhibition for the edges. This parameter is ignored if |

`AdjMat` |
The signed undirected adjacency matrix for the pathway topology. |

`ncomp` |
The pre-specified number of sub-graphs used to calculate the consistency score. Default is using all sub-graphs. |

`data` |
A data frame of gene expression levels, with rows for profile genes and columns for perturbed pathway genes/proteins (column names are the perturbed gene/protein symbols). |

`neigen` |
The maximum number of eigen sub-spaces used to calculate gene scores. Default is using all eigen sub-spaces. |

The consistency score is returned as a list with the length of `ncomp`

(if specified) or the number of sub-graphs in the pathway graph. Each element of the list is either `NULL`

or a data frame. There are three reasons to cause the returned consistency score to be `NULL`

: 1) There is a conflict in the topology; 2) Not sufficient data to calculate the consistency score (less than 2 perturbed genes/proteins connected in the graph); 3) pre-specified `neigen`

is greater than the number of nodes in the graph. The data frame of the non-null score has two columns for the profile gene annotations (rowname of `data`

) and the consistency scores, respectively.

1 2 3 4 5 6 7 8 9 10 11 12 13 | ```
# load data
downloadLINCS("LincsCGS")
Data <- LincsCGS$MCF7
# obtain edge information of a pathway
Edges <- AllEdges[AllEdges$Pathway=="hsa04150",]
# calculate consistency score by specifying edge information
CalcScore(EdgeFrom=Edges$GeneSymbol_a,EdgeTo=Edges$GeneSymbol_b,interaction=Edges$Interaction,data=Data,neigen=1)
# calculate consistency score by specifying adjacency matrix
AdjMat <- CalcAdj(EdgeFrom=Edges$GeneSymbol_a,EdgeTo=Edges$GeneSymbol_b,interaction=Edges$Interaction)
CalcScore(AdjMat=AdjMat,data=Data,neigen=1)
``` |

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