annnotateWithControlDepth: Annotate Case with Control Depth
In VariantTools: Tools for Exploratory Analysis of Variant Calls

Description Usage Arguments Details Value Author(s) See Also Examples

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.

1	annotateWithControlDepth(case, control, control.cov)

`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`.

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.

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

Michael Lawrence

callSampleSpecificVariants, which uses this function.

  bams <- LungCancerLines::LungCancerBamFiles()
  data(vignette)
  case <- callVariants(tallies_H1993)
  control <- tallies_H2073
  control.cov <- coverage(bams$H2073)
  annotateWithControlDepth(case, control, control.cov)