PureCN (version 1.0.3)

readCurationFile: 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.

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)