Hi, I want to know how to set parameter to calculate the motif distance by ALLR(Lower Limit). Thanks. I tried to use MotIV to calculate the motif distance by ALLR. library(MotifDb) TFs <- subset(MotifDb, !is.na(tfFamily)) tfMatrix <- as.list(TFs) tfMatrix <- tfMatrix[sample(1:length(tfMatrix), 20)] library(MotIV) d <- motifDistances(tfMatrix, cc="ALLR") d2 <- motifDistances(tfMatrix, cc="SSD") d3 <- motifDistances(tfMatrix, cc="KL") d4 <- motifDistances(tfMatrix, cc="PCC") Yours sincerely, Jianhong Ou LRB 670A Program in Gene Function and Expression 364 Plantation Street Worcester, MA 01605 [[alternative HTML version deleted]]