CalcScoreSummary: Calculate the summarized consistency score for each gene...

Description Usage Arguments Value Examples

View source: R/CalcScoreSummary.R

Description

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

Usage

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

Arguments

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 AdjMat is specified.

interaction

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

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.

Value

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.

Examples

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# 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.