AnnotationHub-class: AnnotationHub objects and their related methods and functions

In Bioconductor/AnnotationHub: Client to access AnnotationHub resources

AnnotationHub objects and their related methods and functions

Description

Use AnnotationHub to interact with Bioconductor's AnnotationHub service. Query the instance to discover and use resources that are of interest, and then easily download and import the resource into R for immediate use.

Use AnnotationHub() to retrieve information about all records in the hub. If working offline, add argument localHub=TRUE to work with a local, non-updated hub; It will only have resources available that have previously been downloaded. If offline, Please also see BiocManager vignette section on offline use to ensure proper funcionality. To force redownload of the hub, refreshHub(hubClass="AnnotationHub") can be utilized.

If you are operating behind a proxy please see the AnnotationHub Vignette section on "Accessing behind a Proxy" for setting up configuration to allow AnnotationHub to run properly.

Discover records in a hub using mcols(), query(), subset(), and [.

Retrieve individual records using [[. On first use of a resource, the corresponding files or other hub resources are downloaded from the internet to a local cache. On this and all subsequent uses the files are quickly input from the cache into the R session. If a user wants to download the file again and not use the cache version add the argument force=TRUE.

AnnotationHub records can be added (and sometimes removed) at any time. snapshotDate() restricts hub records to those available at the time of the snapshot. possibleDates() lists snapshot dates valid for the current version of Bioconductor. You can check the status of a past record using recordStatus().

The location of the local cache can be found (and updated) with getAnnotationHubCache and setAnnotationHubCache; removeCache removes all cache resources.

For common hub troubleshooting, please see the AnnotationHub vignette entitled 'vignette("TroubleshootingTheHubs", package="AnnotationHub")'.

Constructors

AnnotationHub(..., hub=getAnnotationHubOption("URL"), cache=getAnnotationHubOption("CACHE"), proxy=getAnnotationHubOption("PROXY"), localHub=getAnnotationHubOption("LOCAL")):

Create an AnnotationHub instance, possibly updating the current database of records.

Accessors

In the code snippets below, x and object are AnnotationHub objects.

hubCache(x):

Gets the file system location of the local AnnotationHub cache.

hubUrl(x):

Gets the URL for the online hub.

isLocalHub(x):

Get whether or not constructor was called with localHub=TRUE.

length(x):

Get the number of hub records.

names(x):

Get the names (AnnotationHub unique identifiers, of the form AH12345) of the hub records.

fileName(x):

Get the file path of the hub records as stored in the local cache (AnnotationHub files are stored as unique numbers, of the form 12345). NA is returned for those records which have not been cached.

mcols(x):

Get the metadata columns describing each record. Columns include:

title

Record title, frequently the file name of the object.

dataprovider

Original provider of the resource, e.g., Ensembl, UCSC.

species

The species for which the record is most relevant, e.g., ‘Homo sapiens’.

taxonomyid

NCBI taxonomy identifier of the species.

genome

Genome build relevant to the record, e.g., hg19.

description

Textual description of the resource, frequently automatically generated from file path and other information available when the record was created.

tags

Single words added to the record to facilitate identification, e.g,. TCGA, Roadmap.

rdataclass

The class of the R object used to represent the object when imported into R, e.g., GRanges, VCFFile.

sourceurl

Original URL of the resource.

sourectype

Format of the original resource, e.g., BED file.

dbconn(x):

Return an open connection to the underyling SQLite database.

dbfile(x):

Return the full path the underyling SQLite database.

.db_close(conn):

Close the SQLite connection conn returned by dbconn(x).

Subsetting and related operations

In the code snippets below, x is an AnnotationHub object.

x$name:

Convenient reference to individual metadata columns, e.g., x$species.

x[i]:

Numerical, logical, or character vector (of AnnotationHub names) to subset the hub, e.g., x[x$species == "Homo sapiens"].

x[[i, force=FALSE, verbose=TRUE]]:

Numerical or character scalar to retrieve (if necessary) and import the resource into R. If a user wants to download the file again and not use the cache version add the argument force=TRUE. verbose=FALSE will quiet status messages.

query(x, pattern, ignore.case=TRUE, pattern.op= `&`):

Return an AnnotationHub subset containing only those elements whose metadata matches pattern. Matching uses pattern as in grepl to search the as.character representation of each column, performing a logical `&` across columns. e.g., query(x, c("Homo sapiens", "hg19", "GTF")).

pattern

A character vector of patterns to search (via grepl) for in any of the mcols() columns.

ignore.case

A logical(1) vector indicating whether the search should ignore case (TRUE) or not (FALSE).

pattern.op

Any function of two arguments, describing how matches across pattern elements are to be combined. The default `&` requires that only records with all elements of pattern in their metadata columns are returned. `&`, `|` and `!` are most notably available. See "?&" or ?base::Ops for more information.

subset(x, subset):

Return the subset of records containing only those elements whose metadata satisfies the expression in subset. The expression can reference columns of mcols(x), and should return a logical vector of length length(x). e.g., subset(x, species == "Homo sapiens" & genome=="GRCh38").

recordStatus(hub, record):

Returns a data.frame of the record id and status. hub must be a Hub object and record must be a character(1). Can be used to discover why a resource was removed from the hub.

Cache and hub management

In the code snippets below, x is an AnnotationHub object.

snapshotDate(x):

and snapshotDate(x) <- value: Gets or sets the date for the snapshot in use. value should be one of possibleDates().

possibleDates(x):

Lists the valid snapshot dates for the version of Bioconductor that is being run (e.g., BiocManager::version()).

cache(x):

and cache(x) <- NULL: Adds (downloads) all resources in x, or removes all local resources corresponding to the records in x from the cache. In the later case, x would typically be a small subset of AnnotationHub resources. If x is a subset hub from a larger hub, and localHub=TRUE was used to construct the hubs, the original object will need to be reconstructed to reflect the removed resources. See also removeResources for a nicer interface for removing cached resources, or removeCache for deleting the hub cache entirely.

hubUrl(x):

Gets the URL for the online AnnotationHub.

hubCache(x):

Gets the file system location of the local AnnotationHub cache.

refreshHub(..., hub, cache, proxy, hubClass=c("AnnotationHub", "ExperimentHub")):

Force redownload of Hub sqlite file. This returns a Hub object as if calling the constructor (ie. AnnotationHub()). For force redownload specifically for AnnotationHub the base call should be refreshHub(hubClass="AnnotationHub")

removeResources(hub, ids):

Removes listed ids from the local cache. ids are "AH" ids. Returns an updated hub object. To work with updated hub object suggested syntax is to reassign (ie. hub = removeResources(hub, "AH1")). If ids are missing will remove all previously downloaded local resources.

removeCache(x, ask=TRUE):

Removes local AnnotationHub database and all related resources. After calling this function, the user will have to download any AnnotationHub resources again.

Coercion

In the code snippets below, x is an AnnotationHub object.

as.list(x):

Coerce x to a list of hub instances, one entry per element. Primarily for internal use.

c(x, ...):

Concatenate one or more sub-hub. Sub-hubs must reference the same AnnotationHub instance. Duplicate entries are removed.

Author(s)

Martin Morgan, Marc Carlson, Sonali Arora, Dan Tenenbaum, and Lori Shepherd

See Also

getInfoOnIds

Examples

  ## create an AnnotationHub object
  library(AnnotationHub)
  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)

  ### Examples ###

  ## One can  search the hub for multiple strings
  ahs2 <- query(ah, c("GTF", "77","Ensembl", "Homo sapiens"))

  ## information about the file can be retrieved using
  ahs2[1]

  ## one can further extract information from this show method
  ## like the sourceurl using:
  ahs2$sourceurl
  ahs2$description
  ahs2$title

  ## We can download a file by name like this (using a list semantic):
  gr <- ahs2[[1]]
  ## And we can also extract it by the names like this:
  res <- ah[["AH28812"]]

  ## the gtf file is returned as a GenomicRanges object and contains
  ## data about which organism it belongs to, its seqlevels and seqlengths
  seqinfo(gr)

  ## each GenomicRanges contains a metadata slot which can be used to get
  ## the name of the hub object and other associated metadata.
  metadata(gr)
  ah[metadata(gr)$AnnotationHubName]

  ## And we can also use "[" to restrict the things that are in the
  ## AnnotationHub object (by position, character, or logical vector).
  ## Here is a demo of position:
  subHub <- ah[1:3]

  ## recordStatus
  recordStatus(ah, "TEST")
  recordStatus(ah, "AH7220")

Bioconductor/AnnotationHub documentation built on Nov. 2, 2024, 4:38 p.m.