callAmplificationsInLowPurity: Calling of amplifications in low purity samples

In lima1/PureCN: Copy number calling and SNV classification using targeted short read sequencing

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

lima1/PureCN documentation built on Sept. 17, 2024, 5:48 a.m.