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

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