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# Written by Ashoka D. Polpitiya
# for the Department of Energy (PNNL, Richland, WA)
# Copyright 2007, Battelle Memorial Institute
# E-mail: ashoka.polpitiya@pnl.gov
# Website: http://omics.pnl.gov/software
# -------------------------------------------------------------------------
#
# Licensed under the Apache License, Version 2.0; you may not use this file except
# in compliance with the License. You may obtain a copy of the License at
# http://www.apache.org/licenses/LICENSE-2.0
#
# Kruskal-Walis
KruskalWalis.dialog <- list(
#long.running=TRUE,
label = "Kruskal-Walis Test on Crosstab Data",
x.dataframeItem = "T_Data", label = "Choose Data Crosstab",
signal = c("default", function(item, fEff){
obj.name <- get.value(item)
obj <- safe.eval(obj.name)
if(exists(obj.name)) {
col.key <- get.column.metadata.key(obj)
cmt <- get.column.metadata.table(obj)
if(is.null(cmt))
quick_message("Data Has No Column Metadata Set.\n\nUse Metadata->Column Metadata or File->Load Column Metadata to load factors")
set.value(fEff, colnames(cmt)[!colnames(cmt)%in%col.key])
}
}, "fEff"),
fEff.choiceItem = NULL, label = "Choose One Factor"
)
KruskalWalis <- function(x, fEff)
{
Factors <- get.factors(x)
if(!fEff%in%colnames(Factors)) stop(paste("Can't find factor", fEff, "in data set factors"))
Factors <- Factors[,fEff]
if(0%in%dim(x)) stop("Data frame is too small to use")
retarr <- array(NA, c(dim(x)[1], 2))
rownames(retarr) <- rownames(x)
colnames(retarr) <- c("Count.Observed", "pval")
for (i in 1:dim(x)[1])
{
xx <- x[i,]
retarr[i,] <- c(sum(!is.na(xx)), tryCatch(kruskal.test(xx, Factors, na.action=na.omit)$p.value, error = function(e) NA))
}
attr(retarr, "Row_Metadata") <- attr(x, "Row_Metadata")
return(retarr)
}
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