\name{limma2biomaRt}
\alias{limma2biomaRt}
\alias{limma2biomaRt.na}
%- Also NEED an '\alias' for EACH other topic documented here.
\title{ Function to Create HTML Tables from limma Objects using biomaRt
  for Annotation }
\description{
  This function is designed to take an \code{ExpressionSet} and an \code{lmFit}, \code{model.matrix},
  and contrast object from limma and convert into HTML and text tables using
  biomaRt. The alternate function \code{limma2biomaRt.na} is designed to
  be run without user intervention.
}
\usage{
limma2biomaRt(eset, fit, design, contrast, species, links = linksBM()[1:3],
otherdata = annBM()[1:3], ann.source = "entrezgene", adjust = "fdr",
number = 30, pfilt = NULL, fldfilt = NULL, tstat = TRUE,
pval = TRUE, FC = TRUE, expression = TRUE, html = TRUE, text = TRUE,
save = FALSE, addname = NULL, interactive = TRUE, affyid = FALSE)
}
%- maybe also 'usage' for other objects documented here.
\arguments{
  \item{eset}{ An \code{ExpressionSet} containing affymetrix
    expression values. }
  \item{fit}{An \code{lmFit} object. }
  \item{design}{ A \code{model.matrix} object. }
  \item{contrast}{A contrasts matrix from limma. }
  \item{species}{The species name. This must be in a particular format
    for biomaRt. An example for human is "hsapiens", or for mouse
    "mmusculus".}
  \item{links}{A character vector of things to annotate with hyperlinks
    to online databases. See \code{linksBM} for possible values.}
  \item{otherdata}{A character vector of things to annotate with text
    only (i.e., no hyperlinks). See \code{annBM} for possible values.}
  \item{ann.source}{The annotation source of the IDs that will be used
    to annotate the genes. The default value is "entrezgene". See
    details for other possibilities.}
  \item{adjust}{ Multiplicity adjustment. Choices are
    "fdr","holm","hommel","bonferroni", or "none". Partial matching allowed. }
  \item{number}{ Number of genes to output to table. See
    details for more information. }
  \item{pfilt}{ A p-value to filter output. See details
    for more information. }
  \item{fldfilt}{ A fold change to filter output. See
    details for more information. }
  \item{tstat}{Boolean: Output t-statistics in table? Defaults to \code{FALSE}. }
  \item{pval}{Boolean: Output (adjusted) p-values in table?
    Defaults to \code{FALSE}. }
  \item{FC}{Boolean: Output fold changes in table? Defaults to \code{FALSE}. }
  \item{expression}{ Boolean: Output expression values in
    table? Defaults to \code{TRUE}. }
  \item{html}{Boolean: Output data in HTML tables? Defaults to
    \code{TRUE}. }
  \item{text}{Boolean: Output data in text tables? Defaults to \code{TRUE}}
  \item{save}{ Boolean: Save tables as R objects for further
    processing? Defaults to \code{FALSE}. }
  \item{addname}{ A character vector to add to the end of
  the automatically generated output file names. Useful for multiple
  calls to eliminate over-writing of existing HTML or text tables.}
  \item{interactive}{Boolean: Is this an interactive call, or run as
    part of a script (e.g., in an \code{Sweave} document)? Defaults to
    \code{TRUE}}
  \item{affyid}{Boolean. Are the IDs used to annotate these data
    Affymetrix IDs?}
}
\details{
  This function is designed to automatically output HTML tables,
  with filenames taken from the column names of the contrast matrix. The
  number of genes output can be controlled several different
  ways. First, if pfilt and fldfilt are both \code{NULL}, the top genes
  will be output based on the \code{number} variable. Otherwise, the
  genes are filtered based on p-value, fold change, or both. If the
  genes are filtered this way, the number of genes to be output will be
  listed and the filter(s) can then be adjusted if necessary.

  This function currently only supports Affymetrix data. It
  is designed for Affymetrix chips that don't have an
  annotation package, which includes data that have been analyzed using
  the 're-mapped' CDFs supplied to BioC by MBNI at University of
  Michigan.

  The IDs that will be used to annotate the genes depend on the source
  of the data. If, for example, one is using an Affymetrix chip that
  doesn't have a BioC annotation package, then the IDs will be
  Affymetrix IDs. To find out the correct name to use for the ann.source
  argument, one can create a connection to a Biomart database using
  \code{\link[biomaRt]{useMart}} and then get a list of available Affy
  arrays using \code{\link[biomaRt]{listFilters}}.

  If one is using one of the re-mapped CDFs from MBNI at University of
  Michigan, then the IDs to use depend on the mapping used to create the
  CDF. At this time, only three types of CDFs can be used; EntrezGene,
  UniGene, and RefSeq. One can determine the correct ann.source argument
  by creating a connection to a Biomart database, and then calling
  \code{linksBM(mart, linksBM())[[3]]}.
  
}
\value{
 If \code{save} is \code{TRUE}, a list of tables from
 \code{\link[limma:toptable]{topTable}} will be output.
}

\author{ James W. MacDonald <jmacdon@med.umich.edu> }

\seealso{ \code{\link[limma:toptable]{topTable}},
  \code{\link[annaffy]{aafTableAnn}}}
 

\keyword{ manip }% at least one, from doc/KEYWORDS