validatedSignatures {GenomicSuperSignature} | R Documentation

## Validation result in data frame

### Description

Validation result in data frame

### Usage

    validatedSignatures(
      val_all,
      num.out = 5,
      scoreCutoff = NULL,
      swCutoff = NULL,
      clsizeCutoff = NULL,
      indexOnly = FALSE,
      whichPC = NULL
    )

### Arguments

`val_all` | An output matrix from `validate` function. If this input is from multiple datasets, only `scoreCutoff` argument will be considered and other inputs will be ignored.
`num.out` | A number of highly validated RAVs to output. Default is 5. If any of the cutoff parameters are provided, `num.out` or the number of filtered RAVs, whichever smaller, will be chosen.
`scoreCutoff` | A numeric value for the minimum correlation. For multi-studies case, the default is 0.7.
`swCutoff` | A numeric value for the minimum average silhouette width.
`clsizeCutoff` | An integer value for the minimum cluster size.
`indexOnly` | A logical. Under the default (= `FALSE`), the detailed information on validated RAVs, such as score, average silhouette width, cluster size, is printed. If it is set TRUE, only the RAV number will be printed.
`whichPC` | An integer value between 1 and 8. PC number of your data to check the validated signatures with. Under the default (`NULL`), it outputs top scored signatures with any PC of your data.

### Value

A subset of the input matrix, which meets the given condition.

### Examples

    data(miniRAVmodel)
    library(bcellViper)
    data(bcellViper)
    val_all <- validate(dset, miniRAVmodel)
    validatedSignatures(val_all, num.out = 3, scoreCutoff = 0)

[Package GenomicSuperSignature version 1.0.1 Index]