Description Usage Arguments References Examples
Gene Expression Signature Similarity based on Parametric Analysis of Gene Set Enrichment.
1 2 3 4 |
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 |
gene_up |
a up-regulated gene symbol name vector |
gene_dn |
a down-regulated gene symbol name vector |
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.
1 2 3 4 5 6 7 | 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)
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