pwmsDistanceMatrix: Multiple PWMs alignment

In DiffLogo: DiffLogo: A comparative visualisation of biooligomer motifs

Description

Creates a distance matrix for pwms

Usage

pwmsDistanceMatrix(pwms, diagonal_value = 0,
  bottom_default_value = NULL, divergence = shannonDivergence,
  unaligned_penalty = divergencePenaltyForUnaligned,
  try_reverse_complement = TRUE, base_distribution = NULL,
  length_normalization = FALSE)

Arguments

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

Value

list

Author(s)

Lando Andrey

DiffLogo documentation built on Nov. 8, 2020, 6:09 p.m.