getGeneFeatures {GOSim} | R Documentation |
Computes feature vectors for list of genes: Each gene is represented by a vector describing the presence/absence of all GO terms. The absence of each GO term is additionally weighted by its information content.
getGeneFeatures(genelist, pca=FALSE, normalization=FALSE, verbose=FALSE)
genelist |
character vector of Entrez gene IDs |
pca |
perform PCA on feature vectors to reduce dimensionality |
normalization |
scale the feature vectors to norm 1 |
verbose |
print out additional information |
The PCA postprocessing determines the principal components that can explain at least 95% of the total variance in the feature space.
matrix with rows being genes and columns being GO terms.
The result depends on the currently set ontology ("BP","MF","CC").
Holger Froehlich
M. Mistry, P Pavlidis, Gene Ontology term overlap as a measure of gene functional similarity, BMC Bioinformatics, 9:327, 2008.
getGeneSimPrototypes
,
selectPrototypes
, getGeneSim
,
getTermSim
, setOntology
# see selectPrototypes