selectLibs {SAGElyzer}R Documentation

Functions to support the widgets of SAGElyzer

Description

SAGElyzer has several widgets that takes inputs from users before performing certain tasks. Functions described in this help documentation provides supports for the widgets. They may have limited reuse values for other purposes.

Usage

selectLibs()
getDBArgs(what = c("map", "counts", "info"))
getUnixDBArgs(binding = "pg")
getBinding(binding = c("pg"))
getWinDBArgs(what = c("map", "counts", "info"))
getTag()
getDefaults()
getSLyzerArgs(argName = "SAGELyzerArgs")
writeSLyzerArgs(args,argName = "SAGELyzerArgs")
modSLyzerArgs(argName, value)
setSLyzerArgs()
runSLyzer()
writeSAGEKNN(knn, targetSAGE)
getSAGEKNN()
getLibCounts()
mapLib2File()
linkTag2UG()
remapTagNUG(mappings)
SAGEFromGEO()
procSAGE()
mapSAGE2UG()
showDBError()
setKNNArgs()
findNG4Tag()

Arguments

what what - a character string that can be "map", "counts", or "info" to indicate the database table to be accessed
binding binding - a character string for the name of the database binding object to be used. "pg" for PostgreSQL is the only one that is currently supported
args args a list of arguments that will be stored in a predefined environment for later usr
argName argName a character string for the name of an element in the stored list of arguments
value value a value to be associated with an element of the stored list of arguments
knn knn a named vector with the names being the tags that are closely related to a given target tag and values being the calculated distances
targetSAGE targetSAGE a character string for the target tag selectd
mappings mappings a matrix with mappings between SAGE tags and UniGene ids

Details

selectLibs allows users to select a set of SAGE libraries from an interactive interface and store the data in an pre-defined environment for later use.

getDBArgs invokes an interactive interface for users to input the arguments for making connections to an existing database. User inputs are stored in a predefined environment for later use. The function calls getUnixDBArgs or getWinDBArgs depending on the type of the operating system.

getUnixDBArgs invokes the interface for getting arguments for making a connection to a database under Unix.

getWinDBArgs invokes an interactive interface for getting arguments for making a connection to a database under windows through an ODBC bridge.

getTag invokes an interfactive interface for users to input the target SAGE tag base on which tags with similar expression pattern will be sought.

getDefaults invokes an interactive interface for users to reset the default values arguments for SAGELyzer.

getSLyzerArgs returns the argument list stored in a predefined environment.

writeSLyzerArgs overwrites the argument list stored in a predefined environment.

modSLyzerArgs modifies the value of a given element of the argument list that is stroed in a predefined environment.

setSLyzerArgs initializes the values of the argument list and store teh list in a predefined environment for later use.

runSLyzer invokes the function SAGELyzer with correct arguments to calculate the nearest neighbor for a given targe tag.

writeSAGEKNN writes the calculated distances for tags that are closely related to the target tag to a predefined environment.

getSAGEKNN gets the value for the nearest neighbor of a target tag that have been stored in a predefined environment.

getLibCounts invokes the interface to show the actual counts of the nearest neighbors of a target tag.

mapLib2File invokes the interface that displays the mapping between the column name of the database table for counts and the original file name that was used to populate the column.

linkTag2UG invokes an HTML page with links of the tags that are closely related to the target tag to UniGene data page for each of the tags.

remapTagNUG returns a matrix with each SAGE tag mapped to a single UniGene id from a matrix where a tag may be mapped to multiple UniGene ids separated by a ";"

SAGEFromGEO invokes the interactive interface to get SAGE libraries from the NCBI web site.

procSAGE process SAGE libraries and write the merged data to a database table.

mapSAGE2UG invokes an interactive interface for taking inputs from users in order to map SAGE tags to UniGene ids and write the mappings to a database table.

Value

getUnixDBArgs returns a list containing

dbname dbname a character string for the name of the database
user user a character string for the name of the user
password password a character string for a password
host host a character string for the domain name or IP address of the host for the database
counts counts a character string for the name of the databsae table storing SGAE count data
info info a character string for the name of the database table storing mapping information and normalization data
map map a character string for the name of the database table storing the mappings between tag and UniGene ids
DSN DSN a character string for the name of data source name
counts counts a character string for the name of the databsae table storing SGAE count data
info info a character string for the name of the database table storing mapping information and normalization data
map map a character string for the name of the database table storing the mappings between tag and UniGene ids


getSLyzerArgs returns a list of arguments that is stroed in a predefined environment.
getSAGEKNN returns a named vector with tag names and their distances to a target tag.
remapTagNUG returns a matrix with two columns.

Note

The functions are part of the Bioconductor project at Dana-Farber Cancer Institute to provide Bioinformatics functionalities through R

Author(s)

Jianhua Zhang

References

http://www.ncbi.nlm.nih.gov/geo

See Also

SAGELyzer, mergeSAGE

Examples

## No examples are provided as the functions may require the support of
## database or human interference

[Package SAGElyzer version 1.4.2 Index]