NetAffxResource-class: Manage NetAffx annotations

Description Objects from the Class Slots Extends Methods Author(s) See Also Examples

Description

This class is for accessing and retrieving NetAffx annotation files for Affymetrix chips. It requires that the user has established an account with Affymetrix. Detailed usage is described in the ‘Annotations with NetAffx’ vignette.

Objects from the Class

Objects are created by calls of the form NetAffxResource(user="[email protected]", password="terces"), as illustrated below and in the 'Annotations with NetAffx vignette.

Slots

user:

Object of class "character" containing the full user name (typically an email address) obtained when the user registers with Affymetrix.

password:

Object of class "character" containing the password associated with the Affymetrix user name. The password is entered and stored in plain text, and should not be considered secure within Bioconductor.

affxLicence:

Object of class "character" containing the licence, obtained from Affymetrix, for retrieving NetAffx annotations. The licence is usually software specific (e.g., for the AffyCompatible package of Bioconductor). Users will not usually change the defeault value.

directory:

Object of class "character", containing the local directory path where the NetAffx data base and annotation files will reside.

annotationsFile:

Object of class "character" containing the file name of the NetAffx data base. Users will not usually change the default value.

affxUrl:

Object of class "character" containing the URL used to download the NetAffx annotations file. Users will not usually change the default value.

Extends

Class "NetAffxCompatibility", directly. Class "AffyCompatible", by class "NetAffxCompatibility", distance 2.

Methods

[[

signature(x = "NetAffxResource", i = "numeric", j = "missing")

[[

signature(x = "NetAffxResource", i = "character", j = "missing"): Retrieve an object representing all NetAffx annotations available for an array. The argument i may be a numeric index or character string corresponding to an array name returned by names(x).

[[

signature(x = "NetAffxResource", i = "numeric", j = "numeric")

[[

signature(x = "NetAffxResource", i = "character", j = "numeric")

[[

signature(x = "NetAffxResource", i = "numeric", j = "character")

[[

signature(x = "NetAffxResource", i = "character", j = "character"): Retrieve an object representing a specific annotation for an array. The argument i may be a numeric index or character string corresponding to an array name returned by names(x). The argument i may be a numeric index or character string corresonding to an annotation returned by description(x[[i]]).

affxLicence

signature(x = "NetAffxResource"): the character string representation of the licence used to access the NetAffx site.

affxUrl

signature(x = "NetAffxResource"): the url used to access the NetAffx site.

annotationsFile

signature(x = "NetAffxResource"): the file name of NetAffx data base, as stored on the local disk of the user.

directory

signature(x = "NetAffxResource"): the directory in wich the NetAffx data base and annotation files are stored on the local disk of the user.

names

signature(x = "NetAffxResource"): the names of the arrays for which annotations are available.

password

signature(x = "NetAffxResource"): The password associated with the user name obtained when the user registered with Affymetrix. The password is entered and stored as plain text, and is not secure.

readAnnotation

signature(netAffxResource = "NetAffxResource", array = "numeric", annotation = "numeric", ...)

readAnnotation

signature(netAffxResource = "NetAffxResource", array = "numeric", annotation = "character", ...)

readAnnotation

signature(netAffxResource = "NetAffxResource", array = "character", annotation = "numeric", ...)

readAnnotation

signature(netAffxResource = "NetAffxResource", array = "character", annotation = "character", ...)

readAnnotation

signature(netAffxResource = "NetAffxResource", array = "missing", annotation = "AffxAnnotation", ...): Read a specific anntotation file as an R object. for the first four methods, array, if present, indexes or names the array while annotation indexes or names the annotation. All methods also accept content = "logical" to indicate whether the content of the file should be returned if possible (content=TRUE, default) or only the path to the local file (content=FALSE) and update = "logical" indicating whether the file should be read from disk if available (update=FALSE, default) or retrieved from the NetAffx web site (update=TRUE). readAnnotation parses CSV, Tabular, and PSI files to data frames, and reads FASTA files to a list of description / sequence pairs (see Biostrings::readFASTA).

The ... argument is passed to corresponding read functions. CSV files are parsed using read.csv(conn, ...), Tabular files with read.delim(conn, ...), PSI files with read.delim(conn, header=FALSE, skip=1, sep="\t", ...), and FASTA with readFASTA(conn, ...).

show

signature(object = "NetAffxResource"): compactly show the NetAffxResource object.

user

signature(x = "NetAffxResource"): The user name (typcially email address) obtained when the user registers with the Affymetrix web site.

Author(s)

Martin Morgan <[email protected]>

See Also

Vignette ‘Annotations with NetAffx’. Affymetrix user login site https://www.affymetrix.com/site/login/login.affx.

.Rprofile for ways to automatically set variables (such as password, and directory) for each session.

Examples

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## password must be obtained by the user
rsrc <- NetAffxResource(user="[email protected]", password=password)
head(names(rsrc))
affxDescription(rsrc[["Bovine"]])
## paradigm to display all elements of 'annotation'
sapply(affxAnnotation(rsrc[["Bovine"]]), force)
## obtain and read a single annotation
anno <- rsrc[["Porcine", "Annotations, CSV format"]]
df <- readAnnotation(rsrc, annotation=anno)

AffyCompatible documentation built on Nov. 1, 2018, 2:24 a.m.