NetAffxResource(user="user@research.org", password="terces"),
as illustrated below and in the `Annotations with NetAffx vignette.user:"character" containing
the full user name (typically an email address) obtained when the
user registers with Affymetrix.password:"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:"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:"character",
containing the local directory path where the NetAffx data base
and annotation files will reside.annotationsFile:"character"
containing the file name of the NetAffx data base. Users will not
usually change the default value.affxUrl:"character" containing
the URL used to download the NetAffx annotations file. Users will
not usually change the default value."NetAffxCompatibility", directly.
Class "AffyCompatible", by class "NetAffxCompatibility", distance 2.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]]).
signature(x = "NetAffxResource"):
the character string representation of the licence used to access
the NetAffx site.signature(x = "NetAffxResource"): the
url used to access the NetAffx site.signature(x = "NetAffxResource"): the
file name of NetAffx data base, as stored on the local disk of the
user.signature(x = "NetAffxResource"): the
directory in wich the NetAffx data base and annotation files are
stored on the local disk of the user.signature(x = "NetAffxResource"): the names of
the arrays for which annotations are available.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.signature(netAffxResource = "NetAffxResource", array = "numeric", annotation = "numeric", ...)signature(netAffxResource = "NetAffxResource", array = "numeric", annotation = "character", ...)signature(netAffxResource = "NetAffxResource", array = "character", annotation = "numeric", ...)signature(netAffxResource = "NetAffxResource", array = "character", annotation = "character", ...)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, ...).
signature(object = "NetAffxResource"): compactly
show the NetAffxResource object.signature(x = "NetAffxResource"): The user name
(typcially email address) obtained when the user registers with
the Affymetrix web site. .Rprofile for ways to automatically set variables (such
as password, and directory) for each session.
## password must be obtained by the user
rsrc <- NetAffxResource(user="mtmorgan@fhcrc.org", 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)
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