rea {vulcan} | R Documentation |
REA Calculates enrichment of groups of objects over a vector of values associated to a population of objects
rea(signatures, groups, sweights = NULL, gweights = NULL, minsize = 1)
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 |
A numeric vector of normalized enrichment scores
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