Description Usage Arguments Value Author(s) Examples
Given a list of genes, the function can be used to find over-represented GO terms. The function is based on topGO package.
1 2 3 |
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
|
statistic |
The test method to use. The details can be find in
the |
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 |
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.
Qiang Hu
1 2 3 4 | #paths <- as.list(KEGGPATHID2EXTID)
#paths <- paths[grep("^hsa", names(paths))]
#allgenes <- unique(unlist(paths))
#ovterms <- ovreGO(genes=paths[[1]], allgenes=allgenes)
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