HitConsensus: Return a numeric measure of whether kmer hits linking two...
In npcooley/SynExtend: Tools for Comparative Genomics

HitConsensus

R Documentation

Return a numeric measure of whether kmer hits linking two genomic features are in linearly similar locations in both features.

Description

This function is designed to work internally to SummarizePairs so it works on relatively simple atomic vectors and has little overhead checking.

Usage

HitConsensus(gene1left,
             gene2left,
             gene1right,
             gene2right,
             strand1,
             strand2,
             hit1left,
             hit1right,
             hit2left,
             hit2right)

Arguments

`gene1left`	Integer; feature bound positions in nucleotide space.
`gene2left`	Integer; feature bound positions in nucleotide space.
`gene1right`	Integer; feature bound positions in nucleotide space.
`gene2right`	Integer; feature bound positions in nucleotide space.
`strand1`	Logical; is feature 1 on the positive or negative strand
`strand2`	Logical; is feature 2 on the positive or negative strand
`hit1left`	Integer; kmer hit bound positions in nucleotide space.
`hit1right`	Integer; kmer hit bound positions in nucleotide space.
`hit2left`	Integer; kmer hit bound positions in nucleotide space.
`hit2right`	Integer; kmer hit bound positions in nucleotide space.

Details

HitConsensus calculates whether the distances between the bounds of a kmer hit and the feature bounds are different between the features linked by the kmer.