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| ### rankprod.R (2008-12-18) | ||
| ### | ||
| ### Two-sided rank products statistic | ||
| ### | ||
| ### Copyright 2008 Korbinian Strimmer | ||
| ### | ||
| ### This function is in part based on code from Henry Wirth. | ||
| ### | ||
| ### This file is part of the `st' library for R and related languages. | ||
| ### It is made available under the terms of the GNU General Public | ||
| ### License, version 3, or at your option, any later version, | ||
| ### incorporated herein by reference. | ||
| ### | ||
| ### This program is distributed in the hope that it will be | ||
| ### useful, but WITHOUT ANY WARRANTY; without even the implied | ||
| ### warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR | ||
| ### PURPOSE. See the GNU General Public License for more | ||
| ### details. | ||
| ### | ||
| ### You should have received a copy of the GNU General Public | ||
| ### License along with this program; if not, write to the Free | ||
| ### Software Foundation, Inc., 59 Temple Place - Suite 330, Boston, | ||
| ### MA 02111-1307, USA | ||
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| rankprod.stat = function (X, L) | ||
| { | ||
| FUN = rankprod.fun(L=L) | ||
| score = FUN(X) | ||
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| return( score ) | ||
| } | ||
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| rankprod.fun <- function (L) | ||
| { | ||
| if (missing(L)) stop("Class labels are missing!") | ||
| L = factor(L) | ||
| cl = levels(L) | ||
| if (length(cl) != 2) stop("Class labels must be specified for two groups, not more or less!") | ||
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| idx1 = which( L == levels(L)[1] ) | ||
| idx2 = which( L == levels(L)[2] ) | ||
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| function(X) | ||
| { | ||
| ranks = array(0, dim=c( ncol(X), length(idx1)*length(idx2) ) ) | ||
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| for( i in 1:length(idx1) ) | ||
| { | ||
| for( j in 1:length(idx2) ) | ||
| { | ||
| index = j+length(idx2)*(i-1) | ||
| ranks[ , index] = rank( -abs( X[idx1[i], ] - X[idx2[j], ] ) ) | ||
| } | ||
| } | ||
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| # geometric mean | ||
| avg.rank = exp(rowMeans(log(ranks))) | ||
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| # return rank complement | ||
| compl.rank = ncol(X)-avg.rank+1 | ||
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| return( compl.rank ) | ||
| } | ||
| } | ||
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| \name{diffmean.stat} | ||
| \alias{diffmean.stat} | ||
| \alias{diffmean.fun} | ||
| \alias{rankprod.stat} | ||
| \alias{rankprod.fun} | ||
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| \title{Difference of Means (``Fold Change'') and Rank Products Statistic} | ||
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| \usage{ | ||
| diffmean.stat(X, L) | ||
| diffmean.fun(L) | ||
| rankprod.stat(X, L) | ||
| rankprod.fun(L) | ||
| } | ||
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| \description{ | ||
| These function compute the difference of group means (``fold change'') and the | ||
| related rank products statistic of Breitling et al. (2004). | ||
| } | ||
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| \arguments{ | ||
| \item{X}{data matrix. Note that the \emph{columns} correspond to variables (``genes'') | ||
| and the \emph{rows} to samples.} | ||
| \item{L}{factor containing class labels for the two groups. } | ||
| } | ||
| \details{ | ||
| \code{diffmean.*} computes the difference of means (i.e. the fold-change for log-transformed data). | ||
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| \code{rankprod.*} computes the two-sided rank products statistic, i.e. the geometric mean of the | ||
| ranks of the pairwise absolute mean differences (Breitling et al. 2004). Note that for consistency with the other functions in this package the \emph{complement} of the averaged ranks is returned | ||
| (i.e. rank 1 becomes \code{ncol(X)}, rank 2 becomes \code{ncol(X)-1}, etc.). | ||
| } | ||
| \value{ | ||
| The *.stat functions directly return the respective statistic for each variable. | ||
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| The corresponding *.fun functions return a function that produces the respective | ||
| statistics when applied to a data matrix (this is very useful for simulations). | ||
| } | ||
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| \references{ | ||
| Breitling, R., et al. 2004. Rank products: a simple, yet powerful, new method | ||
| to detect differentially regulated genes in replicated microarray experiments. | ||
| FEBS Letters \bold{573}:83-9. | ||
| } | ||
| \author{ | ||
| Korbinian Strimmer (\url{http://strimmerlab.org}). | ||
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| This function is in part based on code from Henry Wirth. | ||
| } | ||
| \seealso{\code{\link{studentt.stat}},\code{\link{shrinkt.stat}}.} | ||
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| \examples{ | ||
| # load st library | ||
| library("st") | ||
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| # load Choe et al. (2005) data | ||
| data(choedata) | ||
| X <- choe2.mat | ||
| dim(X) # 6 11475 | ||
| L <- choe2.L | ||
| L | ||
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| # L may also contain some real labels | ||
| L = c("group 1", "group 1", "group 1", "group 2", "group 2", "group 2") | ||
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| # difference of means resp. fold change statistic | ||
| score = diffmean.stat(X, L) | ||
| order(abs(score), decreasing=TRUE)[1:10] | ||
| # [1] 4790 6620 1022 10979 970 35 2693 5762 5885 2 | ||
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| # two-sided rank products statistic | ||
| score = rankprod.stat(X, L) | ||
| order(score, decreasing=TRUE)[1:10] | ||
| # [1] 4790 1022 10979 6620 35 2693 970 5762 5885 2 | ||
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| } | ||
| \keyword{univar} |
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