FilterConstructors {VariantTools} | R Documentation

## Variant Filter Constructors

### Description

These functions construct filters (implemented as functions) suitable for collection into `FilterRules` objects, which are then used to filter variant calls. See examples.

### Usage

    SetdiffVariantsFilter(other)
    MinTotalDepthFilter(min.depth = 10L)
    MaxControlFreqFilter(control, control.cov, max.control.freq = 0.03)
    DepthFETFilter(control, control.cov, p.value.cutoff = 0.05)

### Arguments

`other` | The set of variants (as a `VRanges`) to subtract from the set being filtered.
`min.depth` | The minimum depth for a variant to pass.
`control` | The control set of variants (as a `VRanges`) to use when filtering for case-specific variants.
`control.cov` | The coverage (as an `RleList`) for the sample corresponding to the calls in `control`.
`max.control.freq` | The maximum alt frequency allowed in the control for a variant to be considered case-specific.
`p.value.cutoff` | Passing variants must have a p-value below this value.

### Value

In all cases, a closure that returns a logical vector indicating which elements of its argument should be retained.

### Author(s)

Michael Lawrence

### See Also

There are some convenience functions that construct `FilterRules` objects that contain one or more of these filters. Examples are `VariantQAFilters` and `VariantCallingFilters`.

### Examples

      ## Find case-specific variants in a case/control study
      bams <- LungCancerLines::LungCancerBamFiles()

      data(vignette)
      case <- callVariants(tallies_H1993)
      control <- callVariants(tallies_H2073)

      control.cov <- coverage(bams$H2073)

      filters <-
        FilterRules(list(caseOnly = SetdiffVariantsFilter(control),
                           minTotalDepth = MinTotalDepthFilter(min.depth=10L),
                           maxControlFreq = MaxControlFreqFilter(control,
                               control.cov, max.control.freq=0.03),
                           depthFET = DepthFETFilter(control, control.cov,
                               p.value.cutoff=0.05)
                           ))

      specific <- subsetByFilter(case, filters)

[Package VariantTools version 1.28.1 Index]