ptm (version 0.2.2)

net.go: Gene Ontology Network

Description

Explores the relationship among proteins from a given set.

Usage

net.go(data, threshold = 0.2, silent = FALSE)

Arguments

data

either a vector containing the UniProt IDs (vertices) or the path to the txt or rda file containing them.

threshold

threshold value of the Jaccard index above which two proteins are considered to be linked.

silent

logical, if FALSE print details of the running process.

Value

Returns a list containing (i) the dataframe corresponding to the computed Jaccard matrix, (ii) the adjacency matrix, (iii) a vector containing the vertices, and (iv) a matrix describing the edges of the network.

Details

This function first searches the GO terms for each vertex and then computes the Jaccard index for each protein pair, based on their GO terms. Afterwards, an adjacency matrix is computed, where two proteins are linked if their Jaccard index is greater than the selected threshold.

References

Aledo & Aledo (2020) Antioxidants 9(10), 987.

Rhee et al. (2008) Nature Reviews Genetics 9:509<U+2013>515.

See Also

search.go(), term.go(), get.go(), bg.go(), gorilla()

Examples

# NOT RUN {
net.go(path2data = "./GOvivo.txt")
# }