annotatePFAM: Annotate PFAM domains to BioPlex PPI graph

In ccb-hms/BioPlex: R-side access to BioPlex protein-protein interaction data

Annotate PFAM domains to BioPlex PPI graph

Description

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

Usage

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.

References

BioPlex: https://bioplex.hms.harvard.edu/interactions.php

PFAM: http://pfam.xfam.org

See Also

nodeData

Examples

# (1) Obtain the latest version of the 293T PPI network
bp.293t <- getBioPlex(cell.line = "293T", version = "3.0")

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

# (3) Obtain orgdb package from AnnotationHub
ah <- AnnotationHub::AnnotationHub()
orgdb <- AnnotationHub::query(ah, c("orgDb", "Homo sapiens"))
orgdb <- orgdb[[1]]

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

ccb-hms/BioPlex documentation built on Aug. 5, 2023, 9:15 p.m.