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

In shbrief/GenomicSuperSignature: Interpretation of RNA-seq experiments through robust, efficient comparison to public databases

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)

shbrief/GenomicSuperSignature documentation built on May 3, 2023, 10:07 p.m.