celsiusServer {celsius}R Documentation

Object to hold values pertaining to a Celsius Server

Description

Holds values like the URL needed to reach the server or the default timings for accessing the features and samples for the server etc.

Creating Objects

new('celsiusServer',
celsiusUrl = ...., #URL
platform = ...., #Platform for data retrieval
protocol = ...., #Normalization protocol for the data to be retrieved
stringency = ...., #Stringency setting for annotation retrieval
verbose = ...., #Verbosity preference
transform = ...., #Transform the annotations vector into 0's and 1's
retry = ...., #Number of retry attempts with web server
sampleTime = ...., #estimated time to retrieve a sample
featureTime = ...., #estimated time to retrieve a feature
)

Slots

celsiusUrl
Provide an approriate URL "character" to talk to a celsius server
platform
Provide an approriate affymetrix platform "character" for data retrieval. The preferred format is the affymetrix format, but you can also enter Bioconductor formatted platform names. Default is 'HG-U133A'
protocol
Provide an approriate normalization protocol "character" for the data to be retrieved. Values can be: 'rma','vsn','gcrma','plier' and 'mas5'. Default value is 'rma'.
stringency
Provide an approriate stringency setting "numeric". This is the quality of annotation desired. A higher value results in more NA (un-annotated) values for annotation retrieval. Possible values include: 600,500,400,300,200,100. Default is 500.
verbose
Indicate "logical" whether to print output to the screen whenever data has been retrieved from the DB. Default is FALSE.
transform
Indicate "logical" whether or not to format all annotation mask data into a list of only 0's and 1's (ie. to list NAs and and annotation conficts as 0's) Default is FALSE.
retry
Provide the number of retry attempts "character" for the client to attempt to get data from the web server. Default is 3.
sampleTime
Provide an expected wait time "numeric" to retrieve a sample from this platform (can determine this by using time and the getSampleData() in this library if you REALLY hate waiting)
featureTime
Provide an expected wait time "numeric" to retrieve a feature from this platform (can determine this by using time and the getFeatureData() in this library if you REALLY hate waiting)

Author(s)

Marc Carlson


[Package celsius version 1.0.7 Index]