annotatePFAM {BioPlex} | R Documentation |
This function adds PFAM domain annotations to the node metadata of the BioPlex PPI graph.
annotatePFAM(bp.gr, orgdb)
bp.gr |
an object of class |
orgdb |
an |
An object of class graphNEL
containing PFAM domain annotations
in the nodeData
.
BioPlex: https://bioplex.hms.harvard.edu/interactions.php
PFAM: http://pfam.xfam.org
# (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() AnnotationHub::query(ah, c("orgDb", "Homo sapiens")) orgdb <- ah[["AH92581"]] # (4) Annotate PFAM domains bp.gr <- annotatePFAM(bp.gr, orgdb)