compare_sorted_geneSets: compare_sorted_geneSets

In scsR: SiRNA correction for seed mediated off-target effect

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

genesetA1	vector of sorted genes (character vector)
genesetA2	vector of sorted genes (character vector)
genesetB	vector of genes to be used as reference (character vector)
background	vector of genes to be used as background (character vector)
limA	limit the number of genes of the vector genesetA1 to the first limA genes (integer)
limB	limit the number of genes of the vector genesetB1 to the first limB genes (integer)

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)
                              )

scsR documentation built on April 28, 2020, 7:11 p.m.