CalcTPSig: Calculate the association signature by using topology...

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

Description

Calculate the association signature of a pathway to chemical perturbation signatures

Usage

CalcTPSig(EdgeInfo,pathway="Pathway",EdgeFrom="GeneSymbol_a",EdgeTo="GeneSymbol_b",interaction="Interaction",ncomp=NULL,data,neigen=NULL)

Arguments

EdgeInfo	A data frame containing interaction information of all pathways. Four columns are required in this data frame: pathway annotations, gene symbols of one end of the edges, gene symbols of the other end of the edges, interaction types of the edges.
pathway	A character value for the column name of the pathway ID in the dataframe *EdgeInfo*. Default is "Pathway".
EdgeFrom	A character value for the column name of one end of the edges in the dataframe *EdgeInfo*. Default is "GeneSymbol_a".
EdgeTo	A character value for the column name of the other end of the edges in the dataframe *EdgeInfo*. Default is "GeneSymbol_b".
interaction	A numeric value for the column name of the interaction type in the dataframe *EdgeInfo*. Default is "Interaction".
ncomp	The pre-specified number of sub-graphs used to calculate the consistency score. Default is to use all sub-graphs.
data	A data frame of gene expression levels, with rows for profile genes and columns for chemical perturbations.
neigen	The maximum number of eigen sub-spaces used to calculate gene scores. Default is using all eigen sub-spaces.

Value

The association signature is returned as a data frame with two columns. The first column is the annotations of the chemical perturbations, and the second column is the association scores, which is a measure of the association of a pathway to the perturbations.

Examples

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

# calculate the association signature 
CalcTPSig(EdgeInfo=AllEdges,data=Data,neigen=1)

# calculate the association signature for a specific pathway
pathway <- "hsa04150"
edge <- AllEdges[AllEdges$Pathway==pathway,]
CalcTPSig(EdgeInfo=edge,data=Data,neigen=1)

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