createCurationFile: Create file to curate PureCN results

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

Description

Function to create a CSV file that can be used to mark the correct solution in the output of a runAbsoluteCN run.

Usage

createCurationFile(
  file.rds,
  overwrite.uncurated = TRUE,
  overwrite.curated = FALSE
)

Arguments

file.rds	Output of the runAbsoluteCN function, serialized with saveRDS.
overwrite.uncurated	Overwrite existing files unless flagged as ‘Curated’.
overwrite.curated	Overwrite existing files even if flagged as ‘Curated’.

Value

A data.frame with the tumor purity and ploidy of the maximum likelihood solution.

Author(s)

Markus Riester

See Also

runAbsoluteCN

Examples

data(purecn.example.output)
file.rds <- "Sample1_PureCN.rds"
saveRDS(purecn.example.output, file=file.rds)
createCurationFile(file.rds) 

PureCN documentation built on Nov. 8, 2020, 5:37 p.m.