AAHitScoping: Adjust the scope of kmer hits between feature and genome...

In npcooley/SynExtend: Tools for Comparative Genomics

Adjust the scope of kmer hits between feature and genome space.

Description

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

Usage

AAHitScoping(hitlist,
             fstrand1,
             fstart1,
             fstop1,
             fstrand2,
             fstart2,
             fstop2)

Arguments

hitlist	A list containing matrices produced by SearchIndex.
fstrand1	An integer vector of 0s and 1s describing the strand of features.
fstart1	Integer; a vector of left bounds of features.
fstop1	Integer; a vector of right bounds of features.
fstrand2	An integer vector of 0s and 1s describing the strand of features.
fstart2	Integer; a vector of left bounds of features.
fstop2	Integer; a vector of right bounds of features.

Details

AAHitScoping converts the hits returned by SearchIndex from feature-to-feature context genome-to-genome context.

Value

A list of matrices.

Author(s)

Nicholas Cooley [e-mail]

See Also

NucleotideOverlap, SummarizePairs, WithinSetCompetition, RejectionBy

Examples

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npcooley/SynExtend documentation built on June 8, 2025, 5:24 a.m.