pruneRegulon {viper} | R Documentation |
This function limits the maximum size of the regulons
pruneRegulon(regulon, cutoff = 50, adaptive = TRUE, eliminate = FALSE, wm = NULL)
regulon |
Object of class regulon |
cutoff |
Number indicating the maximum size for the regulons (maximum number of target genes) |
adaptive |
Logical, whether adaptive size should be used (i.e. sum(likelihood^2)) |
eliminate |
Logical whether regulons smalles than |
wm |
Optional numeric vector of weights (0; 1) for the genes |
Prunned regulon
data(bcellViper, package="bcellViper") hist(sapply(regulon, function(x) sum(x$likelihood)/max(x$likelihood)), nclass=20) preg <- pruneRegulon(regulon, 400) hist(sapply(preg, function(x) sum(x$likelihood)/max(x$likelihood)), nclass=20)