my_scripts/annotation_hub.R at master · jdieramon/my_scripts · GitHub

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# Install from Bioconductor
if (!requireNamespace("BiocManager", quietly = TRUE))
  install.packages("BiocManager")

BiocManager::install("AnnotationHub", version = "3.8")


# Load library
library(AnnotationHub)

help("AnnotationHub")


## create an AnnotationHub object
ah = AnnotationHub()

## Summary of available records
ah

## Detail for a single record
ah[1]

## and what is the date we are using?
snapshotDate(ah)

## how many resources?
length(ah)

## from which resources, is data available?
head(sort(table(ah$dataprovider), decreasing=TRUE))

## from which species, is data available ?
head(sort(table(ah$species),decreasing=TRUE))

## what web service and local cache does this AnnotationHub point to?
hubUrl(ah)
hubCache(ah)

## search the hub
cicer <- query(ah, "Cicer arietinum")
pissy <- query(ah, "Aphis gossypii")

# extract information
cicer$dataprovider
cicer$genome
cicer$maintainer

pissy$dataprovider
pissy$genome
pissy$maintainer


# "AnnotationHub" object
class(cicer)
class(pissy)

# retrieve (=download) the element
cicer <- cicer[[1]]
pissy <- pissy[[1]]

#OrgDb object
class(cicer)
cicer

class(pissy)
pissy

# accessing data :
## method columns
columns(cicer)
columns(pissy)

#### method keytypes
keytypes(cicer)
keytypes(pissy)

## method keys
head(keys(cicer, keytype = "GENENAME"))
head(keys(cicer, keytype = "ENTREZID"))
head(keys(cicer, keytype = "SYMBOL"))
head(keys(cicer, keytype = "SYMBOL", pattern = "ARF"))

head(keys(pissy, keytype = "ENTREZID"))
head(keys(pissy, keytype = "SYMBOL"))

# method select
select(cicer, keys = "101509359", keytype = "ENTREZID",
       columns = c("GO", "ONTOLOGY", "SYMBOL"))

select(cicer, keys = "LOC101509359", keytype = "ALIAS",
       columns = c("GO", "CHR", "GENENAME"))

select(pissy, keys = c("114118904", "114118905", "114118906"),
       keytype = "ENTREZID",
       columns = c("GO", "SYMBOL"))


library(dplyr)
select(cicer, keys = "101509359", keytype = "ENTREZID",
       columns = columns(cicer)) %>%
  display()