annnotateWithControlDepth: Annotate Case with Control Depth

In lawremi/VariantTools: Tools for Exploratory Analysis of Variant Calls

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

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

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

lawremi/VariantTools documentation built on March 4, 2024, 11:54 a.m.