readCurationFile {PureCN} | R Documentation

## 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)

[Package PureCN version 1.20.0 Index]