sigGOTable {Ringo} | R Documentation |
Function to obtain a table of significant GO terms given a list of genes, for example: genes related to ChIP-enriched regions.
sigGOTable(selGenes, universeGenes, annotType="list", ontology="BP", maxP=0.001, algorithm="elim", minGenes=10, gene2GO=list(), pkg="org.Mm.eg.db", ...)
selGenes |
character; names of the genes in the list; must
correspond to the names of the list |
universeGenes |
character; names of the genes to focus the analysis on (if desired). Sometimes specifying a smaller list of genes as the background 'universe' may lead to more informative results from the Fisher test. |
annotType |
string; in which format is the GO annotation of the
genes provided; either “list” if a named list (argument
|
ontology |
string; which ontology to use, one of “BP”, “MF”, or “CC” |
maxP |
numeric; which maximum p-value to allow for GO terms to be
called significantly associated to the gene list; passed on topGO
function |
algorithm |
string; one of ‘elim’, ‘classic’, ‘weight’, ‘topgo’, or ‘parentChild’; which method to use in the topGO analyis; see the topGO package for details. |
minGenes |
numeric; the required minimum number of genes
(from |
gene2GO |
A list that contains for each gene the identifiers (GO:00001234...)
of GO terms that are annotated for this gene; only used if
|
pkg |
Name of the Entrezgene-based annotation package to obtain
the GO annotation from. Only used if |
... |
additional arguments that are passed on to the constructor
when building the |
This function is really just a convenience wrapper around functions in
the topGO
package.
It performs an exact Fisher-test and by default uses the ‘elim’
method of the topGO
testing framework.
a data.frame
containing the GO terms with p-values lower than
the specified cut-off.
Joern Toedling
function runTest
and the vignette in package
topGO
## Not run: library("topGO") library("hgu95av2.db") # get probe sets annotated for 'regulation of blood pressure' sel <- get("GO:0007616", hgu95av2GO2ALLPROBES) # create list that matches probe sets to GO ps2GO <- lapply(as.list(hgu95av2GO), names) sigGOTable(selGenes=sel, annotType="list", gene2GO=ps2GO) ## End(Not run)