calculateSimMatrix: calculateSimMatrix Calculate the score similarity matrix...

Description Usage Arguments Details Value Examples

View source: R/rrvgo.R

Description

calculateSimMatrix Calculate the score similarity matrix between terms

Usage

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calculateSimMatrix(
  x,
  orgdb,
  semdata = GOSemSim::godata(orgdb, ont = ont),
  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)

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

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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")

rrvgo documentation built on Nov. 8, 2020, 6:17 p.m.