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

Source: R/findSignature.R

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.

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)
#> [1] "1|2|3|4|5|6|8 (out of 9)"