rea: REA: Rank EnrichmeNt Analysis

In vulcan: VirtUaL ChIP-Seq data Analysis using Networks

Description

REA Calculates enrichment of groups of objects over a vector of values associated to a population of objects

Usage

rea(signatures, groups, sweights = NULL, gweights = NULL,
  minsize = 1)

Arguments

signatures	a named vector, with values as signature values (e.g. logFC) and names as object names (e.g. gene symbols)
groups	a list of vectors of objects (e.g. pathways)
sweights	weights associated to objects in the signature. If NULL (default) all objects are treated according to the signature rank
gweights	weights associated to association strength between each object and each group. If NULL (default) all associations are treated equally
minsize	integer. Minimum size of the groups to be analyzed. Default=1

Value

A numeric vector of normalized enrichment scores

Examples

signatures<-setNames(-sort(rnorm(1000)),paste0('gene',1:1000))
set1<-paste0('gene',sample(1:200,50))
set2<-paste0('gene',sample(1:1000,50))
groups<-list(set1=set1,set2=set2)
obj<-rea(signatures=signatures,groups=groups)
obj

vulcan documentation built on Nov. 8, 2020, 8:15 p.m.