\HeaderA{subColSummarize}{Summarize columns when divided into groups of rows}{subColSummarize}
\aliasA{convert.group.labels}{subColSummarize}{convert.group.labels}
\aliasA{subColSummarizeAvg}{subColSummarize}{subColSummarizeAvg}
\aliasA{subColSummarizeAvgLog}{subColSummarize}{subColSummarizeAvgLog}
\aliasA{subColSummarizeBiweight}{subColSummarize}{subColSummarizeBiweight}
\aliasA{subColSummarizeBiweightLog}{subColSummarize}{subColSummarizeBiweightLog}
\aliasA{subColSummarizeLogAvg}{subColSummarize}{subColSummarizeLogAvg}
\aliasA{subColSummarizeLogMedian}{subColSummarize}{subColSummarizeLogMedian}
\aliasA{subColSummarizeMedian}{subColSummarize}{subColSummarizeMedian}
\aliasA{subColSummarizeMedianLog}{subColSummarize}{subColSummarizeMedianLog}
\aliasA{subColSummarizeMedianpolish}{subColSummarize}{subColSummarizeMedianpolish}
\aliasA{subColSummarizeMedianpolishLog}{subColSummarize}{subColSummarizeMedianpolishLog}
\keyword{univar}{subColSummarize}
\begin{Description}\relax
These functions summarize columns of a matrix when the rows
of the matrix are classified into different groups
\end{Description}
\begin{Usage}
\begin{verbatim}subColSummarizeAvg(y, group.labels)
       subColSummarizeAvgLog(y, group.labels)
       subColSummarizeBiweight(y, group.labels)
       subColSummarizeBiweightLog(y, group.labels)
       subColSummarizeLogAvg(y, group.labels)
       subColSummarizeLogMedian(y, group.labels)
       subColSummarizeMedian(y, group.labels)
       subColSummarizeMedianLog(y, group.labels)
       subColSummarizeMedianpolish(y, group.labels)
       subColSummarizeMedianpolishLog(y, group.labels)
       convert.group.labels(group.labels)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{y}] A numeric \code{\LinkA{matrix}{matrix}}
\item[\code{group.labels}] A vector to be treated as a factor variable. This
is used to assign each row to a group. NA values should be used to
exclude rows from consideration
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
These functions are designed to summarize the columns of a matrix
where the rows of the matrix are assigned to groups. The summarization
is by column across all rows in each group.
\Itemize{
\item[subColSummarizeAvg] Summarize by taking mean
\item[subColSummarizeAvgLog] \code{log2} transform the data and
then take means in column-wise manner
\item[subColSummarizeBiweight] Use a one-step Tukey Biweight to
summarize columns
\item[subColSummarizeBiweightLog] \code{log2} transform the data and
then use a one-step Tukey Biweight to
summarize columns
\item[subColSummarizeLogAvg] Summarize by taking mean and then
taking \code{log2}
\item[subColSummarizeLogMedian] Summarize by taking median and then
taking \code{log2}
\item[subColSummarizeMedian] Summarize by taking median
\item[subColSummarizeMedianLog] \code{log2} transform the data and
then summarize by taking median
\item[subColSummarizeMedianpolish] Use the median polish to
summarize each column, by also using a row effect (not returned)
\item[subColSummarizeMedianpolishLog] \code{log2} transform the
data and then use the median polish to summarize each column, by
also using a row effect (not returned)
}
\end{Details}
\begin{Value}
A \code{\LinkA{matrix}{matrix}} containing column summarized data. Each row
corresponds to data column summarized over a group of rows.
\end{Value}
\begin{Author}\relax
B. M. Bolstad <bmb@bmbolstad.com>
\end{Author}
\begin{Examples}
\begin{ExampleCode}
### Assign the first 10 rows to one group and
### the second 10 rows to the second group
###
y <- matrix(c(10+rnorm(50),20+rnorm(50)),20,5,byrow=TRUE)

subColSummarizeAvgLog(y,c(rep(1,10),rep(2,10)))
subColSummarizeLogAvg(y,c(rep(1,10),rep(2,10)))
subColSummarizeAvg(y,c(rep(1,10),rep(2,10)))

subColSummarizeBiweight(y,c(rep(1,10),rep(2,10)))
subColSummarizeBiweightLog(y,c(rep(1,10),rep(2,10)))

subColSummarizeMedianLog(y,c(rep(1,10),rep(2,10)))
subColSummarizeLogMedian(y,c(rep(1,10),rep(2,10)))
subColSummarizeMedian(y,c(rep(1,10),rep(2,10)))


subColSummarizeMedianpolishLog(y,c(rep(1,10),rep(2,10)))
subColSummarizeMedianpolish(y,c(rep(1,10),rep(2,10)))



\end{ExampleCode}
\end{Examples}