calculateSimMatrix: calculateSimMatrix Calculate the score similarity matrix...

In imbforge/rrvgo: Reduce + Visualize GO

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")

imbforge/rrvgo documentation built on Oct. 24, 2024, 12:18 a.m.