View source: R/GOAssociation.R
GOAssociation | R Documentation |
The GOAssociation function will identify the associated GO terms for each module from the NetSAM or MatSAM function.
GOAssociation(NetSAMOutput, outputHtmlFile, organism, outputType, fdrmethod, fdrth, topNum)
NetSAMOutput |
The list object outputted from the NetSAM or MatSAM function. |
outputHtmlFile |
The output directory of the HTML file. |
organism |
The organism of the input data matrix that has been used to identify the modules. Currently, the package supports the following nine organisms: hsapiens, mmusculus, rnorvegicus, drerio, celegans, scerevisiae, cfamiliaris, dmelanogaster and athaliana. The default is "hsapiens". |
outputType |
The function supports two types of output results. 1. "significant" represents all associated GO terms should be significant under a certain FDR threshold; 2. "top" represents the function first sorts all GO terms based on their hypergenometric test p values and then selects top GO terms as the associated terms. The default is "significant". |
fdrmethod |
The FDR method for identifying the significantly associated GO terms. The default is "BH". |
fdrth |
The FDR threshold. |
topNum |
The number of the selected top GO terms. |
The function will output a data.frame object and a HTML file to show the associated GO terms for each module.
Jing Wang
MatSAM
NetSAM
data(NetSAMOutput_Example)
outputHtmlFile <- paste(getwd(),"/GOAsso_HTML",sep="")
GOAsso <- GOAssociation(NetSAMOutput=netsam_output, outputHtmlFile=outputHtmlFile, organism="hsapiens", fdrmethod="BH", fdrth=0.05, topNum=5)
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