pfm_to_pwm: Convert PFM to PWM.

In mPloenzke/learnMotifs: Learn Nucleotide Motifs via Convolutions

Description

Convert position frequency matrix into a position weight matrix.

Usage

pfm_to_pwm(motif.raw, motif.pos = NULL, mmax, bg = c(0.25, 0.25, 0.25,
  0.25), pseudoprob = 0.001)

Arguments

motif.raw	List of annotated motifs as PFMs.
motif.pos	Vector of indices to extract motifs. If NULL all motifs will be selected.
mmax	Maximum motif length, found via find_max_length.
bg	Vector of background nucleotide probabilities (A, C, G, T)
pseudoprob	Value to add to zero-valued position probability matrix entries prior to converting to PWM.

Value

4-D array containing PWMs of the extracted motifs.

Author(s)

Matthew Ploenzke, [e-mail]

See Also

find_max_length

mPloenzke/learnMotifs documentation built on May 27, 2019, 11:55 a.m.