aggregateGeneSetScores: Take difference of two paired bi-directional gene set scores

In montilab/K2Taxonomer: Creating annotated submodules of high-throughput data through recursive partitioning

Take difference of two paired bi-directional gene set scores

Description

Replaces gene set results from paired up- and down- gene sets with the difference of the up-regulated genes and down-regulated genes

Usage

aggregateGeneSetScores(K2res, aggList)

Arguments

K2res	A K2 class object.
aggList	A named list where each item is a character vector of length, 2, comprising the name of the 'up' gene set, and the name of the 'down' gene set.

Value

An object of class K2.

References

\insertRef

reed_2020K2Taxonomer \insertRefgsvaK2Taxonomer

Examples

## Read in ExpressionSet object
library(Biobase)
data(sample.ExpressionSet)

## Pre-process and create K2 object
K2res <- K2preproc(sample.ExpressionSet)

## Run K2 Taxonomer algorithm
K2res <- K2tax(K2res,
            stabThresh=0.5)

## Run differential analysis on each partition
K2res <- runDGEmods(K2res)

## Create dummy set of gene sets
DGEtable <- getDGETable(K2res)
genes <- unique(DGEtable$gene)
genesetsMadeUp <- list(
    GS1=genes[1:50],
    GS2=genes[51:100],
    GS3=genes[101:150])

## Run gene set hyperenrichment
K2res <- runGSEmods(K2res,
                genesets=genesetsMadeUp,
                qthresh=0.1)

## Run GSVA on genesets
K2res <- runGSVAmods(K2res,
                ssGSEAalg='gsva',
                ssGSEAcores=1,
                verbose=FALSE)

## Aggregate paired gene sets
aggList <- list(c('GS12', 'GS1', 'GS2'))
K2res <- aggregateGeneSetscores(K2resaggList, K2res)

montilab/K2Taxonomer documentation built on April 5, 2025, 3:58 a.m.