ovreGO: Function to analyze over-represented GO terms for a giving...

Description Usage Arguments Value Author(s) Examples

View source: R/ovreGO.R

Description

Given a list of genes, the function can be used to find over-represented GO terms. The function is based on topGO package.

Usage

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ovreGO(genes, allgenes, ontology = "BP", algorithm = "parentchild",
statistic = "fisher", map = "org.Hs.eg.db", nterm = 100, plot = FALSE,
nword = 30, min.freq = 1, scale = c(2, 0.5), ...)

Arguments

genes

The gene set to analyze over-represented GO terms.

allgenes

The background gene set compared to the interested gene set. It can be all GO annotated genes.

ontology

The GO ontology.

algorithm

The details of algorithm can be find in the runTest function from the topGO package.

statistic

The test method to use. The details can be find in the runTest function.

map

The GO annotation package

nterm

The number of top over-represented GO terms.

plot

Wether to plot the returned GO terms. If TRUE, the wordcloud will be plotted.

nword

The maximum character length of GO terms in the wordcloud plot.

min.freq

words with frequency below min.freq will not be plotted

scale

A vector of length 2 indicating the range of the size of the words.

...

More options for wordcloud function.

Value

A data frame from GenTable function of topGO package. Two more colummn "Score" and "wScore" are added to list the significant scores and LC weighted scores. If the plot option is TRUE, a wordcloud will be plotted based on the over-represented GO terms and its weighted significant scores.

Author(s)

Qiang Hu

Examples

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#paths <- as.list(KEGGPATHID2EXTID)
#paths <- paths[grep("^hsa", names(paths))]
#allgenes <- unique(unlist(paths))
#ovterms <- ovreGO(genes=paths[[1]], allgenes=allgenes)

FSim documentation built on May 2, 2019, 6:30 p.m.