findKeywordInRAV {GenomicSuperSignature} | R Documentation

## Find the rank of your keyword in the RAV's GSEA annotation

### Description

Once you provide RAVmodel, keyword you're searching for, and the RAV number to this function, it will give you the abs(NES)-based rank of your keyword in the enriched pathways of the target RAV. If can be useful to find out how uniquely your keyword-containing pathways are represented.

### Usage

    findKeywordInRAV(RAVmodel, keyword, ind, n = NULL, includeTotal = TRUE)

### Arguments

`RAVmodel` | PCAGenomicSignatures-object.
`keyword` | A character vector. If you are searching for multiple keywords at the same time, use `paste` with `collapse="|"` argument.
`ind` | An integer. The RAV number you want to check.
`n` | An integer. The number of top enriched pathways (based on abs(NES)) to search. Under default (`NULL`), all the enriched pathways are used.
`includeTotal` | Under the default condition (`TRUE`), the total number of enriched pathways will be also printed out as a part of the output.

### Value

A character containing the rank of keyword-containing pathways (separated by |), followed by the total number of enriched pathways in parenthesis.

### Examples

    data(miniRAVmodel)
    findKeywordInRAV(miniRAVmodel, "Bcell", ind = 695)

[Package GenomicSuperSignature version 1.2.1 Index]