compare_sorted_geneSets

Description

This method can be used to compare the performances of two different sorted gene vectors (A1 and A2) relative to a reference vector (B). To perform the comparison we use n best hits from genesetA1 and genesetA2. n is defined as the number of elements of the smallest of the two vectors(after intersecting it with the background). For the comparison see also the enrichment_geneSet method.

Usage

compare_sorted_geneSets(genesetA1, genesetA2, genesetB, background, limA=NULL, limB=NULL)

Arguments

Author(s)

Andrea Franceschini

Examples

data(uuk_screen)
data(uuk_screen_dh) 
compare_sorted_geneSets(unique(uuk_screen$GeneID)[1:200], 
                        unique(arrange(add_rank_col(uuk_screen), log_pval_rsa)$GeneID)[1:200], 
                              unique(uuk_screen_dh$GeneID)[1:400], 
                              intersect(uuk_screen$GeneID, uuk_screen_dh$GeneID)
                              )

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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> library(scsR)
Error in library(scsR) : there is no package called 'scsR'
Execution halted