R/FisherLSD.R

In MAIT: Statistical Analysis of Metabolomic Data

##
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## All code copyright (c) 2013 UPC/UB
## All accompanying written materials copyright (c) 2013 UPC/UB
##
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##   This program is free software: you can redistribute it and/or modify
##    it under the terms of the GNU General Public License as published by
##    the Free Software Foundation, either version 2 of the License, or
##    (at your option) any later version.
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##    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.
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##    You should have received a copy of the GNU General Public License
##    along with this program.  If not, see <http://www.gnu.org/licenses/>.
##


FisherLSD <- function(data,classes,index,DFerror,MSerror,numClasses){
	LSD <- LSD.test(y=data[index,],trt=classes,DFerror=DFerror,MSerror=MSerror);
	LSD$groups$trt<- rownames(LSD$groups)
	LSD$groups$M<- LSD$groups$groups
	LSD <- LSD$groups[order(LSD$groups$trt),]
	groups <- paste(LSD$M[1],LSD$M[2],sep=" ")
	for (i in c(3:(numClasses))){
		groups <- paste(groups,LSD$M[i],sep=" ")
	}
	out <- list(LSD$trt,groups,LSD$means)
	names(out) <- c("trt","group","means")
	return(out)
}