propTests {Rariant} | R Documentation

## Testing Functions

### Description

Vectorized implementation of testing functions

### Usage

    scoreTest(x1, n1, x2, n2)

    nmTest(x1, n1, x2, n2, delta = 0)

    feTest(x1, n1, x2, n2, ...)

### Arguments

`x1` | Mismatch counts in the test sample.
`n1` | Sequencing depth (total counts) in the test sample.
`x2` | Mismatch counts in the control sample.
`n2` | Sequencing depth (total counts) in the control sample.
`delta` | Difference to test against (default: 0).
`...` | Additional arguments.

### Details

These functions implement a vectorized version of the two-sided (a) Score test and (b) Miettinen-Nurminen test for the difference between to Binomial proportions.

Usage of the score test is discouraged in the settings considered here, since it is ill-defined for positions with no mismatches.

### Value

A data frame with columns

- dhatEstimate for the difference of rates 'p1' and 'p2'.

- p1, p2Estimates for the mismatches rates for each sample.

- tvalT-value

- pvalP-value

### References

Miettinen, Olli, and Markku Nurminen. Comparative Analysis of Two Rates. Statistics in Medicine 4, no. 2 (1985): 213–226. doi:10.1002/sim.4780040211.

### See Also

VariantTools package

### Examples

    ## Generate sample data
    counts = data.frame(x1 = 1:5, n1 = 30, x2 = 0:4, n2 = 30)

    ## Score test
    stat_st = with(counts, scoreTest(x1, n1, x2, n2))

    ## NM test
    stat_nm = with(counts, nmTest(x1, n1, x2, n2))

    ## Fisher test
    stat_fet = with(counts, feTest(x1, n1, x2, n2))

    print(stat_st)

    print(stat_nm)

    print(stat_fet)

[Package Rariant version 1.25.0 Index]