betabinLRT {deepSNV} | R Documentation

## ShearwaterML

### Description

Maximum likelihood version of Shearwater producing p-values instead of Bayes factors.

### Usage

    betabinLRT(
      counts,
      rho = NULL,
      truncate = 0.05,
      rho.min = 1e-04,
      rho.max = 0.8,
      maxvaf = 0.3,
      mindepth = 10,
      maxtruncate = 0.5
    )

### Arguments

`counts` | The array of counts typically generated by loadAllData.
`rho` | Use this variable to fix the dispersion parameter to a value of interest. Default: NULL, rho will be estimated from the data.
`truncate` | Samples with variant allele frequencies higher than "truncate" will be excluded from the background error model.
`rho.min` | If rho=NULL, rho will be estimated from the data in the interval [rho.min,rho.max].
`rho.max` | If rho=NULL, rho will be estimated from the data in the interval [rho.min,rho.max].
`maxvaf` | Sites with an average rate of mimatches higher than maxvaf will not be considered (e.g. SNPs or reference sites).
`mindepth` | Minimum coverage required to test a site.
`maxtruncate` | Maximum number of samples that can be excluded from the background error model by truncate for a site to be tested.

### Value

A list with two arrays for P- and Q-values.

### Author(s)

Inigo Martincorena and Moritz Gerstung

### References

Martincorena I, Roshan A, Gerstung M, et al. (2015). High burden and pervasive positive selection of somatic mutations in normal human skin. _Science_ (Under consideration).

### Examples

    # code to be added

[Package deepSNV version 1.40.0 Index]