page: Gene Expression Signature Similarity

In zhilongjia/scorePage: Gene Expression Signature Similarity based on Parametric Analysis of Gene Set Enrichment

Description

Gene Expression Signature Similarity based on Parametric Analysis of Gene Set Enrichment.

Usage

page1(datM, geneV, center = TRUE, isRank = TRUE, adjust = "fdr")

page2(datM, gene_up, gene_dn, center = TRUE, isRank = TRUE,
  adjust = "fdr")

Arguments

datM	A Gene Expression Signature matrix including logFC or rank
geneV	a gene symbol name vector
center	boolean - median center gene expression matrix columns prior to analysis.
isRank	datM is rank or not (the top one up-regualted gene has rank 1).
adjust	p.adjust.methods. see p.adjust
gene_up	a up-regulated gene symbol name vector
gene_dn	a down-regulated gene symbol name vector

References

1. Kim, Seon-Young, and David J. Volsky. "PAGE: parametric analysis of gene set enrichment." BMC bioinformatics 6.1 (2005): 1.

2. Iorio, Francesco, et al. "Discovery of drug mode of action and drug repositioning from transcriptional responses." Proceedings of the National Academy of Sciences 107.33 (2010): 14621-14626.

Examples

data(Psoriasis_Etanercept_LogFC)
datM <- apply(-Psoriasis_Etanercept_LogFC, 2, rank)
gene_up <- names(head(sort(Psoriasis_Etanercept_LogFC[,1], decreasing=TRUE), 100) )
gene_dn <- names(head(sort(Psoriasis_Etanercept_LogFC[,1], decreasing=FALSE), 100) )
page1(datM, gene_up)
page1(datM, gene_dn)
page2(datM, gene_up, gene_dn)

zhilongjia/scorePage documentation built on May 4, 2019, 11:22 p.m.