wilcox.evaluate.core {EvaluateCore}

R Documentation

Wilcoxon Rank Sum Test

Description

Compare the medians of quantitative traits between entire collection (EC) and core set (CS) by Wilcoxon rank sum test or Mann-Whitney-Wilcoxon test or Mann-Whitney U test (Wilcoxon 1945; Mann and Whitney 1947).

Usage

wilcox.evaluate.core(data, names, quantitative, selected)

Arguments

data	The data as a data frame object. The data frame should possess one row per individual and columns with the individual names and multiple trait/character data.
names	Name of column with the individual names as a character string
quantitative	Name of columns with the quantitative traits as a character vector.
selected	Character vector with the names of individuals selected in core collection and present in the names column.

Value

Trait	The quantitative trait.
EC_Med	The median value of the trait in EC.
CS_Med	The median value of the trait in CS.
Wilcox_pvalue	The p value of the Wilcoxon test for equality of medians of EC and CS.
Wilcox_significance	The significance of the Wilcoxon test for equality of medians of EC and CS.

References

Mann HB, Whitney DR (1947). “On a test of whether one of two random variables is stochastically larger than the other.” The Annals of Mathematical Statistics, 18(1), 50–60.

Wilcoxon F (1945). “Individual comparisons by ranking methods.” Biometrics Bulletin, 1(6), 80.

See Also

wilcox.test

Examples

####################################
# Use data from R package ccChooser
####################################

library(ccChooser)
data("dactylis_CC")
data("dactylis_EC")

ec <- cbind(genotypes = rownames(dactylis_EC), dactylis_EC[, -1])
ec$genotypes <- as.character(ec$genotypes)
rownames(ec) <- NULL
ec[, c("X1", "X6", "X7")] <- lapply(ec[, c("X1", "X6", "X7")],
                                    function(x) cut(x, breaks = 4))
ec[, c("X1", "X6", "X7")] <- lapply(ec[, c("X1", "X6", "X7")],
                                    function(x) factor(as.numeric(x)))
head(ec)

core <- rownames(dactylis_CC)

quant <- c("X2", "X3", "X4", "X5", "X8")
qual <- c("X1", "X6", "X7")

####################################
# EvaluateCore
####################################

wilcox.evaluate.core(data = ec, names = "genotypes",
                     quantitative = quant, selected = core)

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