GOEnrich.folder-methods: GO enrichment methods

Description

This helper methods can be called to do GO enrichment by using the DAVID web service. GOEnrich.networks can be used to do a GO enrichment of the chromatin maintainer networks. GOEnrich.folder can be called to do a GO enrichment on the gene-list files generated by the method outputGenesPerClusterToDir. There is a 5 secs delay between each request to not avoid being rejected by the server.

Usage

"GOEnrich.folder"(folder, fdr=0.05,GOlimit=20)
"GOEnrich.networks"(object, fdr=0.05, GOlimit= 5,path="")

Arguments

folder

name of the folder that contains the gene-list files. The files are supposed to have a .txt extension. The first column of each file is supposed to contain the genes EntrezID.

object

a "ChromMaintainers" objects with the topNodes already calculated.

fdr

cut-off value GO terms with fdr value

GOlimit

the number of top GO terms to return.

path

the path where to store the generated plot (pdf file). if not specified the plot will be displayed.

Value

Returns a list of data.frame that contain the GO results for each file (or network).

References

http://david.abcc.ncifcrf.gov/ (DAVID website)

Huang DW, Sherman BT, Lempicki RA. Systematic and integrative analysis of large gene lists using DAVID Bioinformatics Resources. Nature Protoc. 2009;4(1):44-57.

Examples

Run this code

    ## get the different datasets path
    petFile <- file.path(system.file("example",package="R3CPET"),"HepG2_interactions.txt")  
    tfbsFile <- file.path(system.file("example",package="R3CPET"),"HepG2_TF.txt.gz")  

 ## Not run: 
# 
#     x <- ChiapetExperimentData(pet = petFile, tfbs=  tfbsFile, IsBed = FALSE, ppiType="HPRD", filter= TRUE) 
#     ## build the different indexes
#     x <- createIndexes(x)
#   
#     ## build networks connecting each interacting regions
#     nets<- buildNetworks(x)
# 
#     ## infer the networks
#     hlda<- InferNetworks(nets)
# 
#     ## Get the list of genes in each cluster by default 
#     ## a folder ClustersGenes will be created
#     outputGenesPerClusterToDir(hlda,x)
# 
#     ## GO enrichment 
#     GOEnrich.folder(folder="ClustersGenes/")
# 
# ## End(Not run)