coverage.evaluate.core {EvaluateCore}

R Documentation

Class Coverage

Description

Compute the Class Coverage (Kim et al. 2007) to compare the distribution frequencies of qualitative traits between entire collection (EC) and core set (CS).

Usage

coverage.evaluate.core(data, names, qualitative, 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
qualitative	Name of columns with the qualitative traits as a character vector.
selected	Character vector with the names of individuals selected in core collection and present in the names column.

Details

Class Coverage (Kim et al. 2007) is computed as follows.

\[Class\, Coverage = \left ( \frac{1}{n} \sum_{i=1}^{n} \frac{A_{CS_{i}}}{A_{EC_{i}}} \right ) \times 100\]

Where, \(A_{CS_{i}}\) is the sets of categories in the CS for the \(i\)th trait, \(A_{EC_{i}}\) is the sets of categories in the EC for the \(i\)th trait and \(n\) is the total number of traits.

Value

The Class Coverage value.

References

Kim K, Chung H, Cho G, Ma K, Chandrabalan D, Gwag J, Kim T, Cho E, Park Y (2007). “PowerCore: A program applying the advanced M strategy with a heuristic search for establishing core sets.” Bioinformatics, 23(16), 2155–2162.

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
####################################

coverage.evaluate.core(data = ec, names = "genotypes",
                       qualitative = qual, selected = core)

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