annotatePFAM | 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
nodeData
# (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)
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