selectLibs {SAGElyzer} | R Documentation |
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.
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()
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 |
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.
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.
The functions are part of the Bioconductor project at Dana-Farber Cancer Institute to provide Bioinformatics functionalities through R
Jianhua Zhang
http://www.ncbi.nlm.nih.gov/geo
## No examples are provided as the functions may require the support of ## database or human interference