wilcox.evaluate.core: 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_individual_1945,mann_test_1947EvaluateCore.

Usage

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

Value

Trait: The quantitative trait.
Count: The accession count (excluding missing data).
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.

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.

References

Examples

Run this code


data("cassava_CC")
data("cassava_EC")

ec <- cbind(genotypes = rownames(cassava_EC), cassava_EC)
ec$genotypes <- as.character(ec$genotypes)
rownames(ec) <- NULL

core <- rownames(cassava_CC)

quant <- c("NMSR", "TTRN", "TFWSR", "TTRW", "TFWSS", "TTSW", "TTPW", "AVPW",
           "ARSR", "SRDM")
qual <- c("CUAL", "LNGS", "PTLC", "DSTA", "LFRT", "LBTEF", "CBTR", "NMLB",
          "ANGB", "CUAL9M", "LVC9M", "TNPR9M", "PL9M", "STRP", "STRC",
          "PSTR")

ec[, qual] <- lapply(ec[, qual],
                     function(x) factor(as.factor(x)))

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