compare_sorted_geneSets {scsR} | R Documentation

## 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

`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)
                                  )

[Package scsR version 1.18.0 Index]