callAmplificationsInLowPurity {PureCN} | R Documentation

## Calling of amplifications in low purity samples

### Description

Function to extract amplification from a `runAbsoluteCN` return object in samples of too low purity for the standard `callAlterations`.

### Usage

    callAmplificationsInLowPurity(
      res,
      normalDB,
      pvalue.cutoff = 0.001,
      percentile.cutoff = 90,
      min.width = 3,
      all.genes = FALSE,
      purity = NULL,
      BPPARAM = NULL
    )

### Arguments

`res` | Return object of the `runAbsoluteCN` function.
`normalDB` | Normal database, created with `createNormalDatabase`.
`pvalue.cutoff` | Copy numbers log-ratio cutoffs to call amplifications as calculating using the log-ratios observed in `normalDB`
`percentile.cutoff` | Only report genes with log2-ratio mean exceeding this sample-wise cutoff.
`min.width` | Minimum number of targets
`all.genes` | If `FALSE`, then only return amplifications passing the thresholds.
`purity` | If not `NULL`, then scale log2-ratios to the corresponding integer copy number. Useful when accurate ctDNA fractions (between 4-10 percent) are available.
`BPPARAM` | `BiocParallelParam` object. If `NULL`, does not use parallelization for fitting local optima.

### Value

A `data.frame` with gene-level amplification calls.

### Author(s)

Markus Riester

### See Also

`runAbsoluteCN` `callAlterations`

### Examples

    data(purecn.example.output)
    normal.coverage.file <- system.file("extdata", "example_normal.txt",
        package="PureCN")
    normal2.coverage.file <- system.file("extdata", "example_normal2.txt",
        package="PureCN")
    normal.coverage.files <- c(normal.coverage.file, normal2.coverage.file)
    normalDB <- createNormalDatabase(normal.coverage.files)
    callAmplificationsInLowPurity(purecn.example.output, normalDB)["EIF2A", ]

[Package PureCN version 1.20.0 Index]