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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
#
# Shapiro Wilks test
ShapiroWilks.dialog <- list(
label = "Shapiro-Wilks Test for Normality of Rows in Crosstab\n",
x.dataframeItem = "T_Data", label = "Choose Data Set",
thres.integerItem = c(value=3, from=0, to=10), label = "At Least This Number Present"
)
ShapiroWilks <- function(x, thres=3)
{
splitIdx <- splitmissing.fLevel(x,thres)
Data.good <- as.matrix(x[splitIdx$good,,drop=FALSE])
Data.bad <- as.matrix(x[splitIdx$bad,,drop=FALSE])
if (dim(Data.bad)[1]==1)
Data.bad <- rbind(Data.bad, Data.bad)
result <- t(t(apply(Data.good, 1,
function(x) { tmp <- shapiro.test(x);
pval <- tmp["p.value"];
return(pval[[1]])})))
normals <- vector(mode="logical", length=length(result))
normals[result > 0.1] <- TRUE
result <- data.frame(normals, result)
colnames(result) <- c("Normal", "pvalue")
attr(result, "Row_Metadata") <- attr(x, "Row_Metadata")
#return(list(pvals=result, miss=Data.bad, allused=(dim(Data.bad)[1]==0)))
return(result)
}
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