Description Usage Arguments Value Examples

View source: R/CalcScoreSummary.R

Calculate the summarized consistency score which is the sum of the consistency scores for all considered sub-graphs.

1 | ```
CalcScoreSummary(EdgeFrom, EdgeTo, interaction, AdjMat = NULL, ncomp = NULL, data, neigen = NULL)
``` |

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

is specified.

`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 summarized consistency score is returned as a data frame with two columns. The first column is the annotations of the profile genes, and the second column is the summarized consistency score.

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 summarized consistency score by specifying edge information
CalcScoreSummary(EdgeFrom=Edges$GeneSymbol_a,EdgeTo=Edges$GeneSymbol_b,interaction=Edges$Interaction,data=Data,neigen=1)
# calculate summarized consistency score by specifying adjacency matrix
AdjMat <- CalcAdj(EdgeFrom=Edges$GeneSymbol_a,EdgeTo=Edges$GeneSymbol_b,interaction=Edges$Interaction)
CalcScoreSummary(AdjMat=AdjMat,data=Data,neigen=1)
``` |

uc-bd2k/paslincs documentation built on Nov. 25, 2019, 8:38 p.m.

Embedding an R snippet on your website

Add the following code to your website.

For more information on customizing the embed code, read Embedding Snippets.