Annotate PFAM domains to BioPlex PPI graph

Source: R/bioplex.R

This function adds PFAM domain annotations to the node metadata of the BioPlex PPI graph.

annotatePFAM(bp.gr, orgdb)

Arguments

bp.gr

an object of class graph storing the BioPlex PPIs. Typically obtained via bioplex2graph.

orgdb

an orgdb object storing annotation data for human.

Value

An object of class graphNEL containing PFAM domain annotations in the nodeData.

See also

nodeData

Examples

# (1) Obtain the latest version of the 293T PPI network
bp.293t <- getBioPlex(cell.line = "293T", version = "3.0")
#> Using cached version from 2023-02-26 15:10:40

# (2) Turn the data into a graph 
bp.gr <- bioplex2graph(bp.293t)

# (3) Obtain orgdb package from AnnotationHub
ah <- AnnotationHub::AnnotationHub()
#> snapshotDate(): 2022-10-31
orgdb <- AnnotationHub::query(ah, c("orgDb", "Homo sapiens"))
orgdb <- orgdb[[1]]
#> loading from cache
#> Loading required package: AnnotationDbi

# (4) Annotate PFAM domains
bp.gr <- annotatePFAM(bp.gr, orgdb)