This repository contains pre-calculated R object files for demo use.
To run netGO, four input data are required as follows: genes, genesets, network, genesetV.
| Data | genes | genesets | network | genesetV |
|---|---|---|---|---|
| Breast Tumor | brca.RData | c2gs.RData | networkString.RData networkHumannet.RData | genesetVString1,2.RData genesetVHumannet1,2.RData |
| P53 | p53.RData | c2gs.RData | networkString.RData networkHumannet.RData | genesetVString1,2.RData genesetVHumannet1,2.RData |
| Diabetes | dg.RData | cpGenesets.RData | networkString.RData networkHumannet.RData | cpgenesetV1,2.RData |
for c5 gene-sets ( gene ontology ), use c5gs.RData and c5genesetV 1~7.RData ( it's string based )
dgans.Rdata is standard positive gene-sets for Diabetes
brcaans.Rdata is standard positive gene-sets for Breast Tumor
or the user can use Breast Tumor data using DownloadExampleData function in netGO (Recommended)
| Data | genes | genesets | network | genesetV |
|---|---|---|---|---|
| ShadowResponse | Aragenes.RData | KEGGara.RData | networkAranet.RData | AragenesetV.RData |
The original genesetV.RData (>25Mb) file was splitted into two to upload to github
So they should be combined using rbind. For example,
load("genesetVString1.RData") # load genesetV1
load("genesetVString2.RData") # load genesetV2
genesetV = rbind(genesetV1,genesetV2)
rm(genesetV1,genesetV2) # for clear memory usage, optionalnetGOVis function requires four data as follows : obj, genes, genesets, network
| Data | obj | genes | genesets | network |
|---|---|---|---|---|
| BreastTumor | brcaresult.RData | brca.RData | c2gs.RData | networkString.RData |
| ShadowResponse | shadowResult.RData | Aragenes.RData | KEGGara.RData | networkAranet.RData |
Note that pre-calculated brcaresult is built for brca[1:30], so only brca[1:30] should be used.
Human : BreastTumor, P53, Diabete
Yeast : ShadowResponse
stringDB, HumanNet, AraNet, YeastNet, MouseNet
Question / Comment / Suggestion : [email protected], [email protected]
Thanks.