build_GO_SS {ViSEAGO} | R Documentation

## build GO Semantic Similarity object.

### Description

Compute the Information content (IC) on the given ontology, and create a `GO_SS-class` object required by `compute_SS_distances` method to compute GO semantic similarity between enriched GO terms or groups of terms.

### Usage

    build_GO_SS(gene2GO, enrich_GO_terms)

    ## S4 method for signature 'gene2GO,enrich_GO_terms'
    build_GO_SS(gene2GO, enrich_GO_terms)

### Arguments

`gene2GO` | a `gene2GO-class` object from `annotate` method.
`enrich_GO_terms` | a `enrich_GO_terms-class` from `merge_enrich_terms` method.

### Details

This method use `annotate` and `merge_enrich_terms` output objects (see Arguments), and compute the Information content (IC) using the internal code of `godata` function from GOSemSim package.

### Value

a `GO_SS-class` object required by `compute_SS_distances`.

### References

Alexa A, Rahnenfuhrer J, Lengauer T. Improved scoring of functional groups from gene expression data by decorrelating GO graph structure. Bioinformatics 2006; 22:1600-1607.

Guangchuang Yu, Fei Li, Yide Qin, Xiaochen Bo, Yibo Wu and Shengqi Wang. GOSemSim: an R package for measuring semantic similarity among GO terms and gene products. Bioinformatics 2010 26(7):976-978.

Herve Pages, Marc Carlson, Seth Falcon and Nianhua Li (2017). AnnotationDbi: Annotation Database Interface. R package version 1.38.0.

### See Also

Other GO_semantic_similarity: `GO_SS-class`, `compute_SS_distances`

### Examples

    ## Not run:
    ###################
    # initialyse object for compute GO Semantic Similarity
    myGOs<-ViSEAGO::build_GO_SS(
        myGENE2GO,
        BP_sResults
    )

    ## End(Not run)
    ###################
    # load data example
    utils::data(
        myGOs,
        package="ViSEAGO"
    )

[Package ViSEAGO version 1.0.0 Index]