GOEnrich.folder-methods {R3CPET} | R Documentation |
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.
## S4 method for signature 'character' GOEnrich.folder(folder, fdr=0.05,GOlimit=20) ## S4 method for signature 'ChromMaintainers' GOEnrich.networks(object, fdr=0.05, GOlimit= 5,path="")
folder |
name of the folder that contains the gene-list files. The files are supposed to
have a |
object |
a |
fdr |
cut-off value GO terms with fdr value <= fdr will be considered. Benjamini-Hochberg FDR is used. |
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. |
Returns a list of data.frame
that contain the GO results for each file (or network).
Mohamed Nadhir Djekidel (nde12@mails.tsinghua.edu.cn)
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.
## 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)