phicoef: Calculate the "phi coefficient" between two binary variables
In GenomicRanges: Representation and manipulation of genomic intervals

Description Usage Arguments Value Author(s) References Examples

The phicoef function calculates the "phi coefficient" between two binary variables.

1	phicoef(x, y=NULL)

x, y

Two logical vectors of the same length. If y is not supplied, x must be a 2x2 integer matrix (or an integer vector of length 4) representing the contingency table of two binary variables.

The "phi coefficient" between the two binary variables. This is a single numeric value ranging from -1 to +1.

H. Pag<c3><a8>s

http://en.wikipedia.org/wiki/Phi_coefficient

set.seed(33)
x <- sample(c(TRUE, FALSE), 100, replace=TRUE)
y <- sample(c(TRUE, FALSE), 100, replace=TRUE)
phicoef(x, y)
phicoef(rep(x, 10), c(rep(x, 9), y))

stopifnot(phicoef(table(x, y)) == phicoef(x, y))
stopifnot(phicoef(y, x) == phicoef(x, y))
stopifnot(phicoef(x, !y) == - phicoef(x, y))
stopifnot(phicoef(x, x) == 1)

Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

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The following objects are masked from 'package:base':

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    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
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Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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Loading required package: IRanges
Loading required package: GenomeInfoDb
[1] -0.09785447
[1] 0.8899124