GO.db: A set of annotation maps describing the entire Gene Ontology assembled using data from GO.
library(GO.db)
class(GO.db)
# [1] "GODb"
# attr(,"package")
# [1] "AnnotationDbi"
# ls and objects return a vector of character strings
# giving the names of the objects in the specified environment.
ls("package:GO.db")
objects("package:GO.db")
keytypes(GO.db) # 基因编号系统名称
columns(GO.db)
#columns shows which kinds of data can be returned for the AnnotationDb object.
#keytypes allows the user to discover which keytypes can be passed in to select or keys and the keytype argument.
keys(GO.db)
keys(GO.db,keytype="TERM")
k <- keys(GO.db, keytype = "GOID")[1:3]
AnnotationDbi::select(GO.db,
keys = k,
columns = c("DEFINITION","TERM","ONTOLOGY"),
keytype="GOID")
AnnotationDbi::select(GO.db, keys=keys(GO.db), columns="TERM")
AnnotationDbi::select(GO.db, keys=keys(GO.db), columns=c(c("SYMBOL","REFSEQ")),
keytype="GOID")
##Convert the object to a list
# GO生物过程(BP)术语与其祖先BP术语之间的关联。
x1 <- as.list(GOBPANCESTOR)
# Remove GO IDs that do not have any ancestor
x1 <- x1[!is.na(x1)]
length(x2)
# This data set gives mappings between GO identifiers and their respective terms.
x2 <- as.list(GOTERM)
参考https://www.bioconductor.org/packages/release/data/annotation/manuals/GO.db/man/GO.db.pdf