\name{SAGELyzer}
\alias{SAGELyzer}
\alias{getSAGESQL}
\alias{getTotalRNum}
\alias{getKNN}
\alias{noChunkKNN}
\alias{chunkKNN}
\alias{findNeighborTags}
\alias{getColNames}
\title{Function to filter out the k nearest neighbors for a given tag}
\description{
  This function finds the k nearest neighbors for a given SAGE tag based
  on the expression of SAGE tags across selected SAGE labraries. The
  calculations are based on data stored in a table in a databse.
}
\usage{
SAGELyzer(dbArgs, targetSAGE, libs = "*", normalize = "min", tagColName
= "tag", k = 500, dist = "euclidean", trans = "sqrt")
getSAGESQL(dbArgs, conn, targetSAGE, libs, tagColName, chunk = FALSE,
cursor = "sageRows", ignorZeros = TRUE, what = c("map", "counts",
"info"))
getTotalRNum(dbArgs, conn, tagColName, what = "counts")
getKNN(dbArgs, targetSAGE, libs, tagColName, normalize, k,
                 dist, trans, max = 10000)
noChunkKNN(dbArgs, conn, targetSAGE, libs, tagColName, normalize, k,
dist, trans)
chunkKNN(dbArgs, conn, targetSAGE, libs, tagColName, normalize, k, dist,
trans, rowNum, max = 50000)
findNeighborTags(targetRow, data, k, NF, dist, trans)
 getColNames(dbArgs, conn, what = "counts")
}

\arguments{
  \item{dbArgs}{\code{dbArgs} a list containing arguments needed to make
    connection to a database and queries against a table. The elements
    include a DSN under Windows and database name, user name, password,
    and host under Unix plus the names for three tables that will be
    used by SAGElyzer}
  \item{targetSAGE}{\code{targetSAGE} a character string for the SAGE
    tag whose neighbors will be sought}
  \item{libs}{\code{libs} a vector of character strings for column names
    of database table where SAGE library data are stored}
  \item{normalize}{\code{normalize} a character string for the means to
    perfrom data normalization. Can be either "min", "max", or "none"}
  \item{tagColName}{\code{tagColName} a character string for the column
    name of a database table where SAGE tags are stored}
  \item{k}{\code{k} an integer for the number of nearest neighbors to be
    sought}
  \item{dist}{\code{dist} a character string corresponding to an
    existing R object for calculating distances between two data sets}
  \item{trans}{\code{trans} a character string corresponding to an
    existing R object that will be used to transform the data}
  \item{conn}{\code{conn} a connection to a database}
  \item{chunk}{\code{chunk} a boolean indicating whether data will be
    processed in chunks to avoid running out space}
  \item{ignorZeros}{\code{ignorZeros} a boolean indicating whether data
    rows with all 0s will be ignored}
  \item{what}{\code{what} a character string for the type of database
    table to use for getting data. Have to be either "map", "counts", or
    "info"}
  \item{max}{\code{max} an integer for the maximum number of data rows
    in a chunk to be processed}
  \item{rowNum}{\code{rowNum} an integer for row number}
  \item{NF}{\code{NF} a vector of numerical data that will be used as
    normalization factor for SAGE counts}
  \item{targetRow}{\code{targetRow} a vector of character strings
    containing data for the target SAGE tag}
  \item{data}{\code{data} a matrix containing SAGE counts across
    selected libraries}
  \item{cursor}{\code{cursor} a character string for the name of a
    cursor to reterive data in chunks from a database table}
}
\details{
  Two database tables (default names "sagecounts" and "sageinfo" have to
  exist (tables can be created using other function in this
  package). One table (sagecounts) contains counts for SAGE tags for
  libraries and the other (sageinfo) contains mappings between column
  names used in "sagecounts" to store data for a given SAGE library.

  Functions in this package are normally called by interactive
  interfaces that are invoked when the package is loaded.
}
\value{
  \code{\link{SAGELyzer}} returns a named vector with SAGE tags being
  the names and the corresponding calculated distances to a given tag
  being the values.

  \code{\link{getSAGESQL}} returns a character string for a SQL
  statement to use to query a database.

  \code{\link{getTotalRNum}} returns an integer for the total row number
  of a database table.
}
\references{\url{www.sagenet.org}}
\author{Jianhua Zhang}

\seealso{\code{\link{SAGE4Unix}}}
\examples{
# No example is given as the code requires data with existing tables
}
\keyword{manip}