readCurationFile: Read curation file

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

Read curation file

Description

Function that can be used to read the curated output of the runAbsoluteCN function.

Usage

readCurationFile(
  file.rds,
  file.curation = gsub(".rds$", ".csv", file.rds),
  remove.failed = FALSE,
  report.best.only = FALSE,
  min.ploidy = NULL,
  max.ploidy = NULL
)

Arguments

file.rds	Output of the runAbsoluteCN function, serialized with saveRDS.
file.curation	Filename of a curation file that points to the correct tumor purity and ploidy solution.
remove.failed	Do not return solutions that failed.
report.best.only	Only return correct/best solution (useful on low memory machines when lots of samples are loaded).
min.ploidy	Minimum ploidy to be considered. If NULL, all. Can be used to automatically ignore unlikely solutions.
max.ploidy	Maximum ploidy to be considered. If NULL, all. Can be used to automatically ignore unlikely solutions.

Value

The return value of the corresponding runAbsoluteCN call, but with the results array manipulated according the curation CSV file and arguments of this function.

Author(s)

Markus Riester

See Also

runAbsoluteCN createCurationFile

Examples

data(purecn.example.output)
file.rds <- "Sample1_PureCN.rds"
createCurationFile(file.rds)
# User can change the maximum likelihood solution manually in the generated
# CSV file. The correct solution is then loaded with readCurationFile.
purecn.curated.example.output <-readCurationFile(file.rds)

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