rea: REA: Rank EnrichmeNt Analysis

Description Usage Arguments Value Examples

Description

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

Usage

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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

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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

federicogiorgi/vulcan documentation built on May 27, 2019, 7:25 a.m.