bbb {deepSNV} | R Documentation

## Bayesian beta-binomal test, codename shearwater

### Description

This is the workhorse of the shearwater test. It computes the Bayes factor for each sample, nucleotide and position of the null-model vs. the alternative of a real variant.

### Usage

    bbb(
      counts,
      rho = NULL,
      alternative = "greater",
      truncate = 0.1,
      rho.min = 1e-04,
      rho.max = 0.1,
      pseudo = .Machine$double.eps,
      return.value = c("BF", "P0", "err"),
      model = c("OR", "AND", "adaptive"),
      min.cov = NULL,
      max.odds = 10,
      mu.min = 1e-06,
      mu.max = 1 - mu.min
    )

### Arguments

`counts` | An `array` of nucleotide counts (samples x positions x 10 nucleotides in forward and reverse orientation), typically from `loadAllData`
`rho` | Disperision factor. If NULL, estimated from the data.
`alternative` | The alternative. Currently only "greater" is implemented.
`truncate` | The model uses a compound control sample which is the sum of all samples with a relative nucleotide frequency below truncate at this locus. Default = 0.1.
`rho.min` | Lower bound for the method of moment estimate of the dispersion factor rho.
`rho.max` | Upper bound for the method of moment estimate of the dispersion factor rho.
`pseudo` | A pseudo count to be added to the counts to avoid problems with zeros.
`return.value` | Return value. Either "BF" for Bayes Factor of "P0" for the posterior probability (assuming a prior of 0.5).
`model` | The null model to use. For "OR" it requires the alternative model to be violated on either of the strands, for "AND" the null is specified such that the error rates of the sample of interest and the compound control sample are identical on both strands. "AND" typically yield many more calls. The most recent addition is "adaptive", which switches from "OR" to "AND", if the coverage is less than min.cov, or if the odds of forward and reverse coverage is greater than max.odds. Default = "OR".
`min.cov` | Minimal coverage to swith from OR to AND, if model is "adaptive"
`max.odds` | Maximal odds before switching from OR to AND if model is "adaptive" and min.cov=NULL.
`mu.min` | Minimum of the error rate mu.
`mu.max` | Maximal error rate mu.

### Value

An `array` of Bayes factors

### Note

Experimental code, subject to changes

### Author(s)

mg14

### Examples

    ## Load data from deepSNV example
    regions <- GRanges("B.FR.83.HXB2_LAI_IIIB_BRU_K034", IRanges(start = 3120, end=3140))
    files <- c(system.file("extdata", "test.bam", package="deepSNV"), system.file("extdata", "control.bam", package="deepSNV"))
    counts <- loadAllData(files, regions, q=10)

    ## Run (bbb) computes the Bayes factor
    bf <- bbb(counts, model = "OR", rho=1e-4)
    vcf <- bf2Vcf(bf, counts, regions, samples = files, prior = 0.5, mvcf = TRUE)

    ## Compare to deepSNV
    bf <- bbb(counts, model = "AND", rho=1e-4)
    dpSNV <- deepSNV(test = files[1], control = files[2], regions=regions, q=10)
    plot(p.val(dpSNV), bf[1,,]/(1+bf[1,,]), log="xy")

[Package deepSNV version 1.40.0 Index]