diffMotif: Motif Difference

In alexjgriffith/mT1: Motifs in Tandem with One Another

Description

Find the distances between two motifs within a subset of the genome represented by fasta. If the distribution of motifs are already known look into mT1:::.motifDiffFromDens.

Usage

diffMotif(fasta, motifs, mloc, cloc, i = 1, j = 2, min = 200,
  combine = "Merged")

Arguments

fasta	A DNAStringSet
motifs	The list of motif Character Atomics
mloc	A list of indicies of each motif in fasta
cloc	A list of indicies of each composite motif in fasta
i	Motif index 1
j	Motif index index 2
min	numerical atomic, minimum length of mloc[[i or j]]
combine	What to do if two motifs occur in the same region Merged|First

Value

A numeric vector with two columns , the first being the genomic index the second being the distance.

alexjgriffith/mT1 documentation built on May 10, 2019, 8:53 a.m.