\HeaderA{write.table}{Write summary of the significant regions to a table}{write.table}
\aliasA{write.table,sigSegments-method}{write.table}{write.table,sigSegments.Rdash.method}
\keyword{IO}{write.table}
\keyword{file}{write.table}
\begin{Description}\relax
Write summary of the significant regions to a table
\end{Description}
\begin{Usage}
\begin{verbatim}
write.table(x, file, append, quote, sep, eol, na, dec, row.names, col.names, qmethod)
## S4 method for signature 'sigSegments':
write.table(x, file="", append = FALSE, quote = 7, sep = "\t", eol = "\n", na = "NA", dec = ".", row.names = TRUE, col.names=c("Status", "Chromosome", "Start", "End", "Average KC score", "Mode KC score", "Probes"), qmethod = c("escape", "double"))
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{x}] The sigSegments object to be summarized
\item[\code{file}] either a character string naming a file or a connection open
for writing.  '""' indicates output to the console.
\item[\code{append}] logical. Only relevant if 'file' is a character string.  If
'TRUE', the output is appended to the file.  If 'FALSE', any
existing file of the name is destroyed.
\item[\code{quote}] a logical value ('TRUE' or 'FALSE') or a numeric vector.  If
'TRUE', any character or factor columns will be surrounded by
double quotes.  If a numeric vector, its elements are taken
as the indices of columns to quote.  In both cases, row and
column names are quoted if they are written.  If 'FALSE',
nothing is quoted.
\item[\code{sep}] the field separator string.  Values within each row of 'x'
are separated by this string.
\item[\code{eol}] the character(s) to print at the end of each line (row).
\item[\code{na}] the string to use for missing values in the data.
\item[\code{dec}] the string to use for decimal points in numeric or complex
columns: must be a single character.
\item[\code{row.names}] either a logical value indicating whether the row names of
'x' are to be written along with 'x', or a character vector
of row names to be written.
\item[\code{col.names}] either a logical value indicating whether the column names
of 'x' are to be written along with 'x', or a character
vector of column names to be written.  See the section on
'CSV files' for the meaning of 'col.names = NA'.
\item[\code{qmethod}] a character string specifying how to deal with embedded
double quote characters when quoting strings.  Must be one of
'"escape"' (default), in which case the quote character is
escaped in C style by a backslash, or '"double"', in which
case it is doubled.  You can specify just the initial letter.
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
Writes a summary of the sigSegments object to file. The resulting table contains 7 columns. The interpretation of the columns is as follows:
\item[Status] Either 'L' for loss or 'G' for gain
\item[Chromosome] The chromosome on which this segment is located
\item[Start] The start position (in base pairs) of the segment on the chromosome
\item[End] The end position of the segment on the chromosome
\item[Average KC score] The average KCsmart score over all base pairs in this segment
\item[Mode KC score] The highest (for gains) or lowest (for losses) KCsmart score over all base pairs in this segment
\item[Probes] All probes from the original data that fall into this segment
\end{Details}
\begin{Author}\relax
Jorma de Ronde
\end{Author}
\begin{SeeAlso}\relax
\code{\LinkA{calcSpm}{calcSpm}}, \code{\LinkA{getSigSegments}{getSigSegments}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
data(hsSampleData)
data(hsMirrorLocs)

spm1mb <- calcSpm(hsSampleData, hsMirrorLocs)

siglevel1mb <- findSigLevelTrad(hsSampleData, spm1mb, n=3)

sigSegments1mb <- getSigSegments(spm1mb, siglevel1mb)
write.table(sigSegments1mb, file=file.path(tempdir(),'sigSegments1mb.txt'))

\end{ExampleCode}
\end{Examples}

