annotateWithControlDepth {VariantTools} | R Documentation

## 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)

[Package VariantTools version 1.28.1 Index]