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

Description

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

Usage

 `1` ```phicoef(x, y=NULL) ```

Arguments

 `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.

Value

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

H. Pagès

Examples

 ``` 1 2 3 4 5 6 7 8 9 10``` ```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) ```

Example output

```Loading required package: stats4

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':

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

Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
rbind, rownames, sapply, setdiff, sort, table, tapply, union,
unique, unsplit, which, which.max, which.min

Attaching package: 'S4Vectors'

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

colMeans, colSums, expand.grid, rowMeans, rowSums