
data(SCOP.fa2GOBP)
Anno
. It has slots for "annoData",
"termData" and "domainData":
annoData
: a sparse matrix of domains X termstermData
: variables describing ontology terms (i.e.
columns in annoData), including: "ID" (i.e. term ID), "Name" (i.e. term
Names), "Namespace" (i.e. term Namespace), and "Distance" (i.e. term
Distance to the ontology root)domainData
: variables describing domains (i.e. rows in
annoData), including: "id" for SCOP sunid, and "level" for SCOP level,
"description" for SCOP descriptionAnno-class
# load data
data(SCOP.fa2GOBP)
SCOP.fa2GOBP
# retrieve info on ontology terms
termData(SCOP.fa2GOBP)
# retrieve info on SCOP domains
domainData(SCOP.fa2GOBP)
# retrieve the first 5 rows and columns of annotation data
x <- annoData(SCOP.fa2GOBP)[1:5,1:5]
x
# convert the above retrieval to the full matrix
as.matrix(x)
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