localPwmAlignment: Align pwms

Description Usage Arguments Value Author(s)

View source: R/pwmAlignment.R

Description

Finds best local alignment for two PWMs.

Usage

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localPwmAlignment(pwm_left, pwm_right, divergence = shannonDivergence,
  unaligned_penalty = divergencePenaltyForUnaligned,
  try_reverse_complement = TRUE, base_distribution = NULL,
  length_normalization = FALSE)

Arguments

pwm_left

first PWM, a matrix of type matrix

pwm_right

first PWM, a matrix of type matrix

divergence

is a measure of difference between two pwm columns. Smaller is more similar. If you want to use non-uniform background distribution, provide your own function.

unaligned_penalty

distance for unaligned columns at edges of matrixes. See divergencePenaltyForUnaligned as an example for providing your own function

try_reverse_complement

If false the alignment will not be performed on reverse complements. If true, the input pwms should have column order of ACTG/ACGU.

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

If true, will minimize the average divergence between PWMs. Otherwise will minimize the sum of divergences between positions. In both cases unalignes positions are compared to base_distribution and are counted when computing the alignment length.

Value

list of length two containing the alignment and the divergence

Author(s)

Lando Andrey


DiffLogo documentation built on Nov. 1, 2018, 2:24 a.m.