readCurationFile {PureCN} | R Documentation |
Function that can be used to read the curated output of the
runAbsoluteCN
function.
readCurationFile( file.rds, file.curation = gsub(".rds$", ".csv", file.rds), remove.failed = FALSE, report.best.only = FALSE, min.ploidy = NULL, max.ploidy = NULL )
file.rds |
Output of the |
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 |
max.ploidy |
Maximum ploidy to be considered. If |
The return value of the corresponding runAbsoluteCN
call, but with the results array manipulated according the curation CSV file
and arguments of this function.
Markus Riester
runAbsoluteCN createCurationFile
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)