CalcNodeScore: Calculate the node contribution score

In uc-bd2k/paslincs: Pathway activity signatures from LINCS L1000 consensus gene signatures

Description

Calculate the node contribution score

Usage

CalcNodeScore(EdgeFrom,EdgeTo,interaction,ncomp=NULL,neigen=NULL,data,node)

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.
ncomp	The pre-specified number of sub-graphs used to calculate the consistency score. Default is using all sub-graphs.
neigen	The maximum number of eigen sub-spaces used to calculate gene scores. Default is using all eigen sub-spaces.
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).
node	A character value of the gene symbol of the node of interest.

Value

A data frame with two columns is returned: the first column is the annotation of the profile genes, and the second column is the node contribution score. In either one of the following two situations, NULL will be returned instead of the data frame: 1) the node of interest is not within the perturbed gene/protein list in the data; 2) at least one of the consistency score data frames for the topologies with and without the node of interest is NULL.

Examples

# load data
downloadLINCS("LincsCGS")
Data <- LincsCGS$MCF7

# obtain edge information of a pathway
Edges <- AllEdges[AllEdges$Pathway=="hsa04150",]

# define a node of interest
Node <- "MTOR"

# calculate node contribution score
CalcNodeScore(EdgeFrom=Edges$GeneSymbol_a,EdgeTo=Edges$GeneSymbol_b,interaction=Edges$Interaction,ncomp=NULL,neigen=1,data=Data,node=Node)

uc-bd2k/paslincs documentation built on May 28, 2020, 8:20 a.m.