ToPASeq (version 1.6.0)

ToPASeq-package: Package for topology-based pathway analysis of microarray and RNASeq data

Description

The package implementats several methods for topology-based pathway analysis of microarray data. The methods present in here are: SPIA, TopologyGSA, DEGraph, Clipper, PWEA, TAPPA, TBS. SPIA, PWEA and TBS were also adapted for RNASeq data.

Details

Package:

ToPASeq

Type:

Package

Version:

1.0

Date:

2014-03-04

License:

AGPL-3

Examples

## Not run: 
# if (require(DEGraph)) {
#   data("Loi2008_DEGraphVignette")
#   pathways<-biocarta[1:10]
#   SPIA(exprLoi2008, classLoi2008,pathways , type="MA", logFC.th=-1, IDs="entrez")
#   DEGraph(exprLoi2008, classLoi2008, pathways, type="MA")
#   TAPPA(exprLoi2008, classLoi2008, pathways, type="MA")
#   TopologyGSA(exprLoi2008, classLoi2008, pathways, type="MA", nperm=200)
#   Clipper( exprLoi2008, classLoi2008+1, pathways,type="MA", test="mean")
#   PWEA(exprLoi2008, classLoi2008, pathways,  type="MA", nperm=100)
#   TBS( exprLoi2008, classLoi2008, pathways, type="MA",  logFC.th=-1, nperm=100)
# }
# if (require(gageData)) {
# 
#  data(hnrnp.cnts)
#  group<-c(rep("sample",4), rep("control",4))
#  SPIA( hnrnp.cnts, group, biocarta[1:10], type="RNASeq",  logFC.th=-1, IDs="entrez", test="limma")
#  DEGraph(hnrnp.cnts, group, biocarta[1:10], type="RNASeq", norm.method="TMM")
#  TAPPA( hnrnp.cnts, group, biocarta[1:10], type="RNASeq", norm.method="TMM")
#  TopologyGSA(hnrnp.cnts, group, biocarta[1:10], type="RNASeq",nperm=200, norm.method="TMM")
#  Clipper(hnrnp.cnts, group,biocarta[1:10], type="RNASeq",  norm.method="TMM")
#  PWEA(hnrnp.cnts, group, biocarta[1:10],  type="RNASeq", test="limma", nperm=100)
#  TBS(hnrnp.cnts, group, biocarta[1:10], type="RNASeq", logFC.th=-1, nperm=100, test="limma")
#  }
# ## End(Not run)