mcc: Compute a Mathews Correlation Coefficient

In bhklab/CoreGx: Classes and Functions to Serve as the Basis for Other 'Gx' Packages

Compute a Mathews Correlation Coefficient

Description

The function computes a Matthews correlation coefficient for two factors provided to the function. It assumes each factor is a factor of class labels, and the enteries are paired in order of the vectors.

Usage

mcc(
  x,
  y,
  nperm = 1000,
  nthread = 1,
  alternative = c("two.sided", "less", "greater"),
  ...
)

Arguments

x, y	factor of the same length with the same number of levels
nperm	numeric number of permutations for significance estimation. If 0, no permutation testing is done
nthread	numeric can parallelize permutation texting using BiocParallels bplapply
alternative	indicates the alternative hypothesis and must be one of ‘"two.sided"’, ‘"greater"’ or ‘"less"’. You can specify just the initial letter. ‘"greater"’ corresponds to positive association, ‘"less"’ to negative association.
...	list Additional arguments

Details

Please note: we recommend you call set.seed() before using this function to ensure the reproducibility of your results. Write down the seed number or save it in a script if you intend to use the results in a publication.

Value

A list with the MCC as the $estimate, and p value as $p.value

Examples

x <- factor(c(1,2,1,2,3,1))
y <- factor(c(2,1,1,1,2,2))
mcc(x,y)

bhklab/CoreGx documentation built on March 14, 2024, 3:04 a.m.