findSignature: Find the RAVs with the keyword-containing enriched pathways

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

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)
findSignature(miniRAVmodel, "Bcell")
findSignature(miniRAVmodel, "Bcell", k = 5)

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