calculateSimMatrix {rrvgo} | R Documentation

## calculateSimMatrix Calculate the score similarity matrix between terms

### Description

calculateSimMatrix Calculate the score similarity matrix between terms

### Usage

    calculateSimMatrix(
      x,
      orgdb,
      keytype = "ENTREZID",
      semdata = GOSemSim::godata(orgdb, ont = ont, keytype = keytype),
      ont = c("BP", "MF", "CC"),
      method = c("Resnik", "Lin", "Rel", "Jiang", "Wang")
    )

### Arguments

`x` | vector of GO terms
`orgdb` | one of org.* Bioconductor packages (the package name, or the package itself)
`keytype` | keytype passed to AnnotationDbi::keys to retrieve GO terms associated to gene ids in your orgdb
`semdata` | object with prepared GO DATA for measuring semantic similarity
`ont` | ontlogy. One of c("BP", "MF", "CC")
`method` | distance method. One of the supported methods by GOSemSim: c("Resnik", "Lin", "Rel", "Jiang", "Wang")

### Details

All similarity measures available are those implemented in the [GOSemSim package](https://www.bioconductor.org/packages/release/bioc/html/GOSemSim.html), namely the Resnik, Lin, Relevance, Jiang and Wang methods. See the [Semantic Similarity Measurement Based on GO](https://www.bioconductor.org/packages/release/bioc/vignettes/GOSemSim/inst/doc/GOSemSim.html#semantic-similarity-measurement-based-on-go) section from the GOSeSim documentation for more details.

### Value

a square matrix with similarity scores between terms

### Examples

    go_analysis <- read.delim(system.file("extdata/example.txt", package="rrvgo"))
    simMatrix <- calculateSimMatrix(go_analysis$ID, orgdb="org.Hs.eg.db", ont="BP", method="Rel")

[Package rrvgo version 1.4.4 Index]