submotif: Check if a motif is present within another motif

In MyersGroup/MotifFinder: A Bayesian, De Novo, Joint Motif Finder

Description

Check if a motif is present within another motif

Usage

submotif(motif, submotif = rbind(c(0, 1, 0, 0), c(0, 0, 1, 0)),
  ispcm = FALSE, probabilistic = TRUE)

Arguments

motif	matrix; position weight matrix to check in
submotif	matrix; motif to search for, format: position weight matrix, n by 4 (A, C, G, T), (output of pcm2pwm) (default finds CpG dinucleotides)
ispcm	logical; if TRUE will convert pcm to pwm (default: FALSE)
probabilistic	logical; if FALSE the sum of the convolution is taken, if TRUE (default), the product of the sum of each row is returned. TRUE will only work if the submotif is itself a pwm rather than a generic kernal.

Value

score of submotif being present in motif

MyersGroup/MotifFinder documentation built on June 7, 2019, 3:42 p.m.