Annotate Case with Control Depth

Description

Matches the case variants to the (typically unfiltered) control variants and returns case, with the additional metadata columns control.alt.depth and control.total.depth, corresponding to altDepth(control) and totalDepth(control), respectively.

Usage

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annotateWithControlDepth(case, control, control.cov)

Arguments

case

The variants of interest, as a VRanges.

control

The control variants, typically unfiltered, as a VRanges.

control.cov

The control coverage, as an RleList.

Details

If a case variant is not found in control, a count of 0 is assigned to control.alt.depth, under the assumption that the control object is not filtered, i.e., it contains the raw tallies.

Value

case, plus two new metadata columns, control.alt.depth and control.total.depth

Author(s)

Michael Lawrence

See Also

callSampleSpecificVariants, which uses this function.

Examples

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  bams <- LungCancerLines::LungCancerBamFiles()
  tally.param <- TallyVariantsParam(gmapR::TP53Genome(), 
                                    high_base_quality = 23L,
                                    which = gmapR::TP53Which())
  case <- callVariants(bams$H1993, tally.param)
  control <- tallyVariants(bams$H2073, tally.param)
  control.cov <- coverage(bams$H2073)
  annotateWithControlDepth(case, control, control.cov)