potra_man: PoTRA.corN

Description Usage Arguments Author(s)

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

1
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 valentine.dinu@asu.edu


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