geneWeight: Calculate gene weight

In JiantaoShi/NetGPA: Network-based Gene Prioritization Analysis (NetGPA)

Description

This function is the core function to calculate weight score for a gene.

Usage

geneWeight(queryIndex, Nref, topIndex, seedList, Pfcutoff)

Arguments

queryIndex	The index of query gene.
Nref	Total number of genes in the database.
topIndex	Top indexes that are associated with queryIndex gene
seedList	A list of intger vectors, each of which represents indexes of seed genes.
Pfcutoff	Percentage of top genes considered, should be less than 0.1.

Value

A vector with 2 variables, Nseeds and Cg.

Author(s)

Jiantao Shi

References

Jiantao Shi: NetGPA, a package for network-based gene prioritization analysis.

Examples

# load package and data
library("NetGPA")
data("Example_NetGPA")

# load data base
data(text_2006_12_NetGPA)

# Compare FGF pathway and a random gene set
exampleSeedFGFR <- Example_NetGPA$Cancer_GeneSet[["SIGNALING_BY_FGFR"]]

pGenes <- intersect(exampleSeedFGFR, colnames(text_2006_12_NetGPA))
rGenes <- sample(colnames(text_2006_12_NetGPA), length(pGenes)) 

res    <- NetGPA(as.list(pGenes), pGenes, text_2006_12_NetGPA, progressBar = FALSE)
pTable <- res$queryTable
pTable$group <- "Pathway"

res    <- NetGPA(as.list(rGenes), rGenes, text_2006_12_NetGPA, progressBar = FALSE)
rTable <- res$queryTable
rTable$group <- "Random"

mT <- rbind(pTable, rTable)

boxplot(-log10(queryP)~group, data = mT, ylab = "-log10(p-value)")

JiantaoShi/NetGPA documentation built on Jan. 1, 2021, 9:14 p.m.