pwmsDistanceMatrix: Multiple PWMs alignment

Description Usage Arguments Value Author(s)

View source: R/pwmAlignment.R

Description

Creates a distance matrix for pwms

Usage

1
2
3
4
5
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. 1, 2018, 2:24 a.m.