findSignature {GenomicSuperSignature} | R Documentation

## Find the RAVs with the keyword-containing enriched pathways

### Description

This function finds RAVs containing the keyword you provide. If you provide "the number of keyword-containing pathways per RAV" in argument `k`, it will give you the RAV number.

### Usage

    findSignature(RAVmodel, keyword, n = 5, k = NULL)

### Arguments

`RAVmodel` | PCAGenomicSignatures-object
`keyword` | A character vector. If you are searching for multiple keywords at the same time, use `paste` with `collapse="|"` argument.
`n` | The number of top ranked (based on abs(NES)) pathways you want to search your keyword
`k` | The number of keyword-containing pathways you want to get the RAV number. Under default (`NULL`), the output will be a data frame with two columns: '# of keyword-containing pathways' and 'Freq'. If you assign the value for this argument, the output will be an integer vector containing the RAV index.

### Value

A data frame or integer vector depending on the parameter `k`.

### Examples

    data(miniRAVmodel)
    library(bcellViper)
    data(bcellViper)
    findSignature(miniRAVmodel, "Bcell")
    findSignature(miniRAVmodel, "Bcell", k = 5)

[Package GenomicSuperSignature version 1.0.1 Index]