GOAssociation: Identify the associated GO terms for each module

In bingzhang16/NetSAM: Network Seriation And Modularization

Identify the associated GO terms for each module

Description

The GOAssociation function will identify the associated GO terms for each module from the NetSAM or MatSAM function.

Usage

	GOAssociation(NetSAMOutput, outputHtmlFile, organism, outputType, fdrmethod, fdrth, topNum)

Arguments

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.

Value

The function will output a data.frame object and a HTML file to show the associated GO terms for each module.

Author(s)

Jing Wang

See Also

MatSAM NetSAM

Examples

	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)

bingzhang16/NetSAM documentation built on April 3, 2024, 3:35 a.m.