calculateSimMatrix {rrvgo} | R Documentation |
calculateSimMatrix Calculate the score similarity matrix between terms
calculateSimMatrix( x, orgdb, semdata = GOSemSim::godata(orgdb, ont = ont), ont = c("BP", "MF", "CC"), method = c("Resnik", "Lin", "Rel", "Jiang", "Wang") )
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") |
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.
a square matrix with similarity scores between terms
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")