FilterConstructors: Variant Filter Constructors

In VariantTools: Tools for Exploratory Analysis of Variant Calls

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)

VariantTools documentation built on Nov. 8, 2020, 8:03 p.m.