potra_man: PoTRA.corN

In PoTRA: PoTRA: Pathways of Topological Rank Analysis

Description

The PoTRA analysis is based on topological ranks of genes in biological pathways. PoTRA can be used to detect pathways involved in disease. The PoTRA package contains one function for creating the PoTRA results object.

Usage

PoTRA.corN(mydata, genelist, Num.sample.normal, Num.sample.case, Pathway.database, PR.quantile)

Arguments

mydata	Dataframe that contains rownames consisting of entrez gene identifiers and columns representing normals and samples from gene expression data.
genelist	Dataframe that consists of a single column of entrez gene identifiers (the same as those found in the rownames(mydata)).
Num.sample.normal	Represents normal samples in the mydata dataframe.
Num.sample.case	Represents case samples in the mydata dataframe.
Pathway.database	Object contains gene lists from KEGG, Reactome, Biocarta and PharmGKB databases, and these are made available through the devel graphite library.
PR.quantile	Object contains the percentile of PageRank scores as a cutoff for hub genes, the recommended percentile is 0.95.

Author(s)

Chaoxing Li, Li Liu, Valentine Dinu [e-mail]

PoTRA documentation built on Nov. 8, 2020, 7:46 p.m.