pwmsDistanceMatrix {DiffLogo} | R Documentation |
Creates a distance matrix for pwms
pwmsDistanceMatrix(pwms, diagonal_value = 0, bottom_default_value = NULL, divergence = shannonDivergence, unaligned_penalty = divergencePenaltyForUnaligned, try_reverse_complement = TRUE, base_distribution = NULL, length_normalization = FALSE)
pwms |
list of pwms |
diagonal_value |
value to put on diagonal. |
bottom_default_value |
value to put on bottom triangle. Set to NULL to get symmetric distance matrix. |
divergence |
divergence measure. |
unaligned_penalty |
is a function for localPwmAlignment. |
try_reverse_complement |
if True, alignment will try reverse complement pwms |
base_distribution |
is a vector of length nrow(pwm) that is added to unaligned columns of pwms for comparing. If NULL, uniform distribution is used |
length_normalization |
is a vector of length nrow(pwm) that is added to unaligned columns of pwms for comparing. If NULL, uniform distribution is used |
list
Lando Andrey