| Title: | R SDK for BaseSpace RESTful API |
|---|---|
| Description: | A rich R interface to Illumina's BaseSpace cloud computing environment, enabling the fast development of data analysis and visualisation tools. |
| Authors: | Adrian Alexa |
| Maintainer: | Jared O'Connell <[email protected]> |
| License: | Apache License 2.0 |
| Version: | 1.49.0 |
| Built: | 2024-07-03 05:02:44 UTC |
| Source: | https://github.com/bioc/BaseSpaceR |
The BaseSpaceR package provides a rich R interface to
Illumina's BaseSpace cloud computing environment, enabling the fast
development of data analysis and visualisation tools.
BaseSpace is Illumina's next-generation sequencing cloud computing environment designed with biologists in mind. Researcher can easily store, analyze, collaborate, and share genetic data (https://basespace.illumina.com).
BaseSpaceR is a SDK ofering methods and data structures for working with the data resources BaseSpace REST API exposes.
Features include:
Persistent connection with the REST server.
Support for the REST API query parameters.
Vectorized operations in line with the R semantic. Allows for queries across multiple Projects, Samples, AppResults, Files, etc.
S4 class system used to represent the BaseSpace data model.
Portability on most platforms: Linux, Windows and Mac OS X.
Adrian Alexa
Maintainer: Adrian Alexa [email protected]
AppAuth-classfor details on how to establish a connection with the BaseSpace server.
Response-classfor details on the structure of the objects and the interface used by the API.
Users-class, Genomes-class,
Runs-class, Projects-class,
Samples-class, Files-class
and AppResults-class
for details on various resources supported by the API.
AppAuth instance with 'browse global' scopeThe aAuth is an instance of a AppAuth object.
It can be used to browse some of the public resources available
in BaseSpace without requireing user authentication.
data(aAuth)data(aAuth)
Build from a pre-generated access token. See
AppAuth-class for code examples on how-to generate
such an object.
data(aAuth) ## print the object aAuthdata(aAuth) ## print the object aAuth
AppAuth classClass to manage client's communication and permissions with BaseSpace REST serve.
signature(x = "AppAuth"): ...
signature(x = "AppAuth"): ...
signature(x = "AppAuth"): ...
Adrian Alexa
https://developer.basespace.illumina.com/docs/content/documentation/rest-api/api-reference
Runs, Projects,
Samples, etc. for examples of objects using the
AppAuth handler.
ServiceURI for a low-level object managing the
REST calls.
showClass("AppAuth") ## load an AppAuth instance containing a pre-generated access token data(aAuth) aAuth hasAccess(aAuth) ## new AppAuth instance using a pre-generated access token my_access_token <- "eee44c28ba0e43a1badb85c5ce7bb94d" myHandle <- AppAuth(access_token = my_access_token) myHandle Users(myHandle) ## using the OAuth v2 workflow ## Not run: ## paste your client_id and client_secret here myAppClientId = "" myAppClientSecret = "" ## instantiate a new AppAuth object myHandle <- AppAuth(client_id = myAppClientId, client_secret = myAppClientSecret, scope = "browse global") ## Open the showed URI in a browser and perform the authentication. requestAccessToken(myHandle) hasAccess(myHandle) ## End(Not run)showClass("AppAuth") ## load an AppAuth instance containing a pre-generated access token data(aAuth) aAuth hasAccess(aAuth) ## new AppAuth instance using a pre-generated access token my_access_token <- "eee44c28ba0e43a1badb85c5ce7bb94d" myHandle <- AppAuth(access_token = my_access_token) myHandle Users(myHandle) ## using the OAuth v2 workflow ## Not run: ## paste your client_id and client_secret here myAppClientId = "" myAppClientSecret = "" ## instantiate a new AppAuth object myHandle <- AppAuth(client_id = myAppClientId, client_secret = myAppClientSecret, scope = "browse global") ## Open the showed URI in a browser and perform the authentication. requestAccessToken(myHandle) hasAccess(myHandle) ## End(Not run)
AppResults and "AppResultsSummary" objectsClasses and methods to handle the AppResults resource.
Adrian Alexa
https://developer.basespace.illumina.com/docs/content/documentation/rest-api/api-reference
showClass("AppAuth")showClass("AppAuth")
AppSessionAuth classExtension of the AppAuth class...
Adrian Alexa
https://developer.basespace.illumina.com/docs/content/documentation/rest-api/api-reference
Runs, Projects,
Samples, etc. for examples of objects using the
AppAuth handler.
ServiceURI for a low-level object managing the
REST calls.
showClass("AppAuth") ## using the OAuth v2 workflow ## Not run: ## paste your client_id and client_secret here myAppClientId = "" myAppClientSecret = "" ## instantiate a new AppAuth object myHandle <- AppAuth(client_id = myAppClientId, client_secret = myAppClientSecret, scope = "browse global") ## Open the showed URI in a browser and perform the authentication. requestAccessToken(myHandle) hasAccess(myHandle) ## End(Not run)showClass("AppAuth") ## using the OAuth v2 workflow ## Not run: ## paste your client_id and client_secret here myAppClientId = "" myAppClientSecret = "" ## instantiate a new AppAuth object myHandle <- AppAuth(client_id = myAppClientId, client_secret = myAppClientSecret, scope = "browse global") ## Open the showed URI in a browser and perform the authentication. requestAccessToken(myHandle) hasAccess(myHandle) ## End(Not run)
AppSessions objectClasses and methods to handle the AppSessions resource.
coming soon...
Adrian Alexa
https://developer.basespace.illumina.com/docs/content/documentation/rest-api/api-reference
showClass("AppAuth")showClass("AppAuth")
This methods are used to provide mean read coverage depth in a particular chromosomal region.
getCoverageStats(x, ...) getCoverage(x, ...)getCoverageStats(x, ...) getCoverage(x, ...)
x |
An object of class |
... |
Adiditional arguments supported by the REST API.
|
Coming soon...
These methods return a list with a representation of coverage histogram.
Adrian Alexa
https://developer.basespace.illumina.com/docs/content/documentation/rest-api/api-reference
data(aAuth) ## get the Ids of some BAM files ##... ## You might require Read access to the AppResult #initializeAuth(aAuth, scope = paste("browse global, read project", 12)) #requestAccessToken(aAuth) #getCoverageStats(aAuth, id = bid, "phix") #readcov <- getCoverage(aAuth, id = bid, "phix", StartPos = 1L, EndPos = 5e3L)[[1]] #barplot(readcov$MeanCoverage, col = "lightblue1", border = NA) #plot(readcov$MeanCoverage, col = "lightblue2", type = "l", lwd = 2)data(aAuth) ## get the Ids of some BAM files ##... ## You might require Read access to the AppResult #initializeAuth(aAuth, scope = paste("browse global, read project", 12)) #requestAccessToken(aAuth) #getCoverageStats(aAuth, id = bid, "phix") #readcov <- getCoverage(aAuth, id = bid, "phix", StartPos = 1L, EndPos = 5e3L)[[1]] #barplot(readcov$MeanCoverage, col = "lightblue1", border = NA) #plot(readcov$MeanCoverage, col = "lightblue2", type = "l", lwd = 2)
Files and FilesSummary objectsClasses and methods to handle the Files resource.
The Files resource provides access to files stored in BaseSpace. A file should be seen as a data stream and associated attributes (date created, size, type, etc.).
Files are associated with specific Runs, Samples, or AppResults and the Files resource provides the interface for manipulating these files.
Adrian Alexa
https://developer.basespace.illumina.com/docs/content/documentation/rest-api/api-reference
AppAuth, Runs,
Samples and AppResults.
data(aAuth) ## get one AppResult reseq <- AppResults(listAppResults(aAuth, projectId = 21383369, Limit = 1)) f <- listFiles(reseq) TotalCount(f) Name(f) identical(f, listFiles(aAuth, appResultId = Id(reseq))) ## list only the BAM files f <- listFiles(aAuth, appResultId = Id(reseq), Extensions = ".bam") Name(f)data(aAuth) ## get one AppResult reseq <- AppResults(listAppResults(aAuth, projectId = 21383369, Limit = 1)) f <- listFiles(reseq) TotalCount(f) Name(f) identical(f, listFiles(aAuth, appResultId = Id(reseq))) ## list only the BAM files f <- listFiles(aAuth, appResultId = Id(reseq), Extensions = ".bam") Name(f)
Files objects and relatedMethods to handle various files types.
The Files resource provides access to files stored in BaseSpace. A file should be seen as a data stream and associated attributes (date created, size, type, etc.).
For known file types (.bam, .vcf, etc.) we offer wrappers to 'map' this objects to various Bioconductor objects.
Adrian Alexa
https://developer.basespace.illumina.com/docs/content/documentation/rest-api/api-reference
AppAuth, AppResults and
Files
data(aAuth) ## get one AppResult reseq <- AppResults(listAppResults(aAuth, projectId = 21383369, Limit = 1)) f <- listFiles(reseq) TotalCount(f) Name(f) ## list only the BAM files f <- listFiles(aAuth, appResultId = Id(reseq), Extensions = ".bam") Name(f) ## construct the BAMFile ##...data(aAuth) ## get one AppResult reseq <- AppResults(listAppResults(aAuth, projectId = 21383369, Limit = 1)) f <- listFiles(reseq) TotalCount(f) Name(f) ## list only the BAM files f <- listFiles(aAuth, appResultId = Id(reseq), Extensions = ".bam") Name(f) ## construct the BAMFile ##...
Genomes and GenomesSummary objectsClasses and methods to handle the Genomes resource.
listGenomes(x, ...) lists all the available genomes, returning
only a small summary for each genome.
is an AppAuth object.
Parameters supported by the REST API, specified as
name = value. For example,
listGenomes(aAuth, Offset = 5, Limit = 2)
Genomes():
Instantiates an empty Genomes object. Same as new("Genomes").
Genomes(x, id):
x is an AppAuth object.
id is either and integer or a character string storing an
integer. id can have length larger that 1.
Genomes(x):
x is an GenomesSummary object.
Adrian Alexa
https://developer.basespace.illumina.com/docs/content/documentation/rest-api/api-reference
data(aAuth) ## list all available genomes g <- listGenomes(aAuth) g$SpeciesName ## using the REST API query parameters listGenomes(aAuth, Limit = 2) g <- listGenomes(aAuth, Offset = 5, Limit = 2, SortBy = "Build") g ## get the details for the listed geneomes Genomes(g) ## get the genomes based on their ID Genomes(aAuth, id = 4) ## if the ID is missing thean NULL is returned for that particular ID Genomes(aAuth, id = c(4, 1, 110))data(aAuth) ## list all available genomes g <- listGenomes(aAuth) g$SpeciesName ## using the REST API query parameters listGenomes(aAuth, Limit = 2) g <- listGenomes(aAuth, Offset = 5, Limit = 2, SortBy = "Build") g ## get the details for the listed geneomes Genomes(g) ## get the genomes based on their ID Genomes(aAuth, id = 4) ## if the ID is missing thean NULL is returned for that particular ID Genomes(aAuth, id = c(4, 1, 110))
This page is used as a placeholder for private methods in order to pass the R checks.
Internal use.
Adrian Alexa
Projects and ProjectsSummary objectsClasses and methods to handle the Projects resource.
The Projects resource provides a logical grouping of the Samples resource and the AppResults resource for a given user.
listProjects(x, ...) lists all the available projects visable
to the user, returning only a small summary for each project.
is an AppAuth object.
Parameters supported by the REST API, specified as
name = value. For example,
listProjects(x, Limit = 2)
Projects():
Instantiates an empty Projects object. Same as new("Projects").
Projects(x, id):
x is an AppAuth object.
id is either and integer or a character string storing an
integer. id can have length larger that 1.
Projetcs(x):
x is an ProjectsSummary object.
Adrian Alexa
https://developer.basespace.illumina.com/docs/content/documentation/rest-api/api-reference
AppAuth, Response,
Users and Runs.
data(aAuth) p <- listProjects(aAuth) p Projects(aAuth, id = c(2, 12, 1012)) Projects(p) ## Make a new project ... createProject(aAuth, name = "My Project X") ## We need 'write global' access to be able to create a new project ## Not run: initializeAuth(aAuth, scope = "write global") requestAccessToken(aAuth) createProject(aAuth, name = "My Project X") ## End(Not run)data(aAuth) p <- listProjects(aAuth) p Projects(aAuth, id = c(2, 12, 1012)) Projects(p) ## Make a new project ... createProject(aAuth, name = "My Project X") ## We need 'write global' access to be able to create a new project ## Not run: initializeAuth(aAuth, scope = "write global") requestAccessToken(aAuth) createProject(aAuth, name = "My Project X") ## End(Not run)
Item, Collection and Response objectsThese virtual classes provide the building blocks for the containers return by quering various BaseSpace resource. They are modeled after the Response container defined by the REST API.
Conceptually there are two response types exposed by BaseSpace, an
individual response and a collection response. The former, modeled by
the Item S4 class, is used when querying an individual
item/instance within a resource. The later is used for listing the
items/instances available for a given resource and is modeled by the
Collection S4 class.
The Item class models a simple unordered set of key/value
pairs. There is a core set of keys, for which access methods are
defined and which are inherited by any child class.
In the following x is an Item object.
$:The $ operator can be used to access the
Item elements. When x is an Item object this is equivalet
to @. But one can think at it as user level operator.
Unlike @ the replace method is not implemented for $.
Id(x):Id of the resource. Character string, though it will always be an integer.
Name(x):Name of the selected resource.
Href(x):Location of the resource in the API. The first component of the URI is the version of the REST API.
DateCreated(x):When this resource was created. Character string. It can be
converted to a Date instace by as.Date(DateCreated(x)).
UserOwnedBy(x):Information about the User who owns this resource. At this moment
this is a list object, but it might be replace with
an object at a future point.
Status(x):The status of the resource. Can be of any type and it will be defined by the classes extended Item.
HrefBaseSpaceUI(x):The location of this project in BaseSpace. Character string giving the complete URL within the BaseSpace dashboard.
The Collection class models an ordered set of Item
objects and a set of predefined attributes. The interface
provided by the Item class is implemented by this class.
However, since we deal with an ordered set of objects, the methods
and the access methods, return a vector of the same length as the
size of the collection.
In the following x is a Collection object.
All accesor implemented by the item class are implemented by
Collection class. However here the return value is a vector. If
x has 2 elements, then Id(x) will be a vector with 2
elements. The same stands for the general accessor $.
length(x):Returns the number of elements in Collection x.
Items(x):List of Item objects.
TotalCount(x):The total number of items in the collection as reported by the queried resource.
Offset(x):The starting point the collection was read from.
Limit(x):The maximum number of items returned. Ranges from 0 to 1024.
SortDir(x):The way the collection is sorted, either ascending or descending.
SortBy(x):The field to use to sort the collection.
Comming soon ...
length(x):Returns the number of elements in Collection x.
show(x):Prints the object.
as.list(x):R list representation of the object.
Adrian Alexa
showClass("Item") showClass("Collection") showClass("Response")showClass("Item") showClass("Collection") showClass("Response")
"ResponseStatus"
The ResponseStatus class is used internally to manage the status messages returned by the REST service.
Objects can be created by calls of the form ResponseStatus().
ResponseStatus() creates an ResponseStatus instances...
signature(x = "ServiceURI"): Returns
TRUE if the HTTP status is 2xx.
signature(object = "ServiceURI"): ...
Adrian Alexa
showClass("ResponseStatus")showClass("ResponseStatus")
Runs and RunsSummary objectsClasses and methods to handle the Runs resource.
The Runs resource contains the raw data produced by the instruments, the base calls, together with run metrics, instrument health data, and other information used for data processing and analysis.
listRuns(x, ...) lists all the available runs visable to the user, returning
only a small summary for each run.
is an AppAuth object.
Parameters supported by the REST API, specified as
name = value. For example,
listRuns(x, Limit = 2, Statuses = "Failed")
Runs():
Instantiates an empty Runs object. Same as new("Runs").
Runs(x, id):
x is an AppAuth object.
id is either and integer or a character string storing an
integer. id can have length larger that 1.
Runs(x):
x is an RunsSummary object.
Adrian Alexa
https://developer.basespace.illumina.com/docs/content/documentation/rest-api/api-reference
data(aAuth) r <- listRuns(aAuth) r listRuns(aAuth, Statuses = "Failed") # no faild runs listRuns(aAuth, Statuses = "Complete") listRuns(aAuth, SortBy = "Id", SortDir="Desc") Runs(r)[[1]] Runs(aAuth, id = 101102) Runs(r) Runs(aAuth, id = c(Id(r), "11111")) # the third element must be NULLdata(aAuth) r <- listRuns(aAuth) r listRuns(aAuth, Statuses = "Failed") # no faild runs listRuns(aAuth, Statuses = "Complete") listRuns(aAuth, SortBy = "Id", SortDir="Desc") Runs(r)[[1]] Runs(aAuth, id = 101102) Runs(r) Runs(aAuth, id = c(Id(r), "11111")) # the third element must be NULL
Samples and SamplesSummary objects Classes and methods to handle the Samples resource.
In general samples are the result of demultiplexing and are thought as the holding the input data for an App. One example of data within a Samples resource are the FASTQ files.
listSamples(x, projectId, ...) lists all the available samples
associated with a particular project. It returns a small summary for
each existing sample.
is an AppAuth object.
the ID of the project we want to explore.
Parameters supported by the REST API, specified as
name = value.
For example, listSamples(x, projectId = "1", Limit = 2)
listSamples(x, ...)
is an Projects object.
Parameters supported by the REST API.
Samples():
Instantiates an empty Samples object. Same as new("Samples").
Samples(x, id):
x is an AppAuth object.
id is either and integer or a character string storing an
integer. id can have length larger that 1.
Samples(x):
x is an SamplesSummary object.
Adrian Alexa
https://developer.basespace.illumina.com/docs/content/documentation/rest-api/api-reference
data(aAuth) ## list all the available projects and select one p <- Projects(listProjects(aAuth, Limit = 1), simplify = TRUE) p ## list the samples available in this project allS <- listSamples(aAuth, projectId = Id(p)) ## we can call listSamples() directly using 'p' identical(allS, listSamples(p)) oneS <- listSamples(aAuth, projectId = Id(p), Limit = 1) oneS Samples(oneS) # list with one Samples object Samples(oneS, simplify = TRUE) # Samples objectdata(aAuth) ## list all the available projects and select one p <- Projects(listProjects(aAuth, Limit = 1), simplify = TRUE) p ## list the samples available in this project allS <- listSamples(aAuth, projectId = Id(p)) ## we can call listSamples() directly using 'p' identical(allS, listSamples(p)) oneS <- listSamples(aAuth, projectId = Id(p), Limit = 1) oneS Samples(oneS) # list with one Samples object Samples(oneS, simplify = TRUE) # Samples object
"ServiceURI"
The ServiceURI class is a general container for storing the URI of a REST based Web service.
Objects can be created by calls of the form ServiceURI().
ServiceURI() creates an ServiceURI instances out of
an URL and an API resource.
url:Object of class "character" ~~
version:Object of class "character" ~~
signature(object = "ServiceURI"): ...
signature(x = "ServiceURI"): ...
Adrian Alexa
showClass("ServiceURI")showClass("ServiceURI")
Users objects and resourcesClass to manage the Users resource.
The Users resource allows the client to get basic information about the user that is currently using the application.
To query this resource we use the Users() method.
Users():
Instantiates an empty Users object. Same as new("Users").
Users(x):
x is an AppAuth object. The function returns a
Response object of class Users.
Adrian Alexa
https://developer.basespace.illumina.com/docs/content/documentation/rest-api/api-reference
data(aAuth) ## Empty instance Users() ## Quering the Users resource using the AppAuth handler u <- Users(aAuth) ## Printing the object shows the response elements u ## Accesors Id(u) Name(u) ## Using the general '$' accesor, same interface as 'list' u$Id u$Email # there is no accesor method Email(), so '$' is useful here! u$fakeElement # returns NULL (to keep the same semantic as 'list') ## Quering the resource unsing a Response object Users(u) # u is of class Users which extends Response ## Specifying a user ID. ID can be specify either as an integer or as a string Users(aAuth, id = 1463464) # must work if given as an integer(even of mode numeric) Users(aAuth, id = "1463464") # must work ## This should fail since is not the current user tryCatch(Users(aAuth, id = "660666"), error = function(e) cat("No access to this user data!\n"))data(aAuth) ## Empty instance Users() ## Quering the Users resource using the AppAuth handler u <- Users(aAuth) ## Printing the object shows the response elements u ## Accesors Id(u) Name(u) ## Using the general '$' accesor, same interface as 'list' u$Id u$Email # there is no accesor method Email(), so '$' is useful here! u$fakeElement # returns NULL (to keep the same semantic as 'list') ## Quering the resource unsing a Response object Users(u) # u is of class Users which extends Response ## Specifying a user ID. ID can be specify either as an integer or as a string Users(aAuth, id = 1463464) # must work if given as an integer(even of mode numeric) Users(aAuth, id = "1463464") # must work ## This should fail since is not the current user tryCatch(Users(aAuth, id = "660666"), error = function(e) cat("No access to this user data!\n"))
Manipulating variant data.
getVariantSet(x, ...) getVariants(x, ...)getVariantSet(x, ...) getVariants(x, ...)
x |
An object of class |
... |
Adiditional arguments supported by the REST API.
|
Coming soon...
These methods return a list with a representation of variant data.
Adrian Alexa
https://developer.basespace.illumina.com/docs/content/documentation/rest-api/api-reference
data(aAuth) ## get the ids of VCF files (within an AppResult? ) reseq <- listAppResults(aAuth, projectId = 21383369, Limit = 1) AppResults(reseq) vcfs <- listFiles(AppResults(reseq), Extensions = ".vcf") Name(vcfs) Id(vcfs) vcfs ## Not run: ## variant metadata getVariantSet(aAuth, vid) ## get the variants getVariants(aAuth, vid, chrom = "chr") v <- getVariants(aAuth, vid, chrom = "chr", EndPos = 1000000L, Limit = 5) v ## End(Not run)data(aAuth) ## get the ids of VCF files (within an AppResult? ) reseq <- listAppResults(aAuth, projectId = 21383369, Limit = 1) AppResults(reseq) vcfs <- listFiles(AppResults(reseq), Extensions = ".vcf") Name(vcfs) Id(vcfs) vcfs ## Not run: ## variant metadata getVariantSet(aAuth, vid) ## get the variants getVariants(aAuth, vid, chrom = "chr") v <- getVariants(aAuth, vid, chrom = "chr", EndPos = 1000000L, Limit = 5) v ## End(Not run)