qvals2Vcf {deepSNV} | R Documentation

## Function to create a `VCF` object with variant calls from an array of q-values.

### Description

This function thresholds the q-values computed by the shearwater algorithm and creates a `VCF` object as output.

### Usage

    qvals2Vcf(
      qvals,
      counts,
      regions,
      samples = 1:nrow(counts),
      err = NULL,
      mu = NULL,
      cutoff = 0.05,
      mvcf = TRUE
    )

### Arguments

`qvals` | array of q-values from `betabinLRT`.
`counts` | array of counts from `loadAllData`.
`regions` | `GRanges` with the regions corresponding to counts and qvals.
`samples` | vector of samples names.
`err` | Optional matrix of error rates, otherwise recomputed from counts.
`mu` | Optional matrix of relative frequencies, otherwise recomputed from counts.
`cutoff` | Cutoff for the q-values below which a variant is considered to be true (default = 0.05)
`mvcf` | boolean flag, if TRUE compute a large VCF with as many genotype columns as samples. Default TRUE. Otherwise use duplicate rows and only one genotype column. The sample is then provided by the info:PD field. Can be inefficient for large sample sizes.

### Value

A `VCF` object

### Note

Experimental code, subject to changes

### Author(s)

mg14

[Package deepSNV version 1.40.0 Index]