cosinePerm {PharmacoGx} | R Documentation

## Cosine Permuations

### Description

Computes the cosine similarity and significance using permutation test. This function uses random numbers, to ensure reproducibility please call `set.seed()` before running the function.

### Usage

    cosinePerm(
      x,
      y,
      nperm = 1000,
      alternative = c("two.sided", "less", "greater"),
      include.perm = FALSE,
      nthread = 1
    )

### Arguments

`x` | `factor` is the factors for the first variable
`y` | `factor` is the factors for the second variable
`nperm` | `integer` is the number of permutations to compute the null distribution of MCC estimates
`alternative` | `string` 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. Options are 'two.sided', 'less', or 'greater'
`include.perm` | `boolean` indicates whether the estimates for the null distribution should be returned. Default set to 'FALSE'
`nthread` | `integer` is the number of threads to be used to perform the permutations in parallel

### Value

A `list` estimate of the cosine similarity, p-value and estimates after random permutations (null distribution) in include.perm is set to 'TRUE'

### Examples

    x <- factor(c(1,2,1,2,1))
    y <- factor(c(2,2,1,1,1))
    cosinePerm(x, y)

[Package PharmacoGx version 2.0.9 Index]