R: Calling of amplifications in low purity samples

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)

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.

Value

A data.frame with gene-level amplification calls.

Author(s)

Markus Riester

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 1.17.1 Index]