genome.delta_star_profile {sigma_difference} R Documentation

Sliding window ``delta*`` profile: the delta-difference between each local

Description

window of the genome and the comparison sequence.<br /><br /> PERFORMANCE: implemented with the incremental window count matrix<br /> (O(1) update per slide + O(16) distance per sample), and the comparison<br /> sequence signature is built only once.

Usage

genome.delta_star_profile(genome, compare,
    windowsSize = 1000);

Arguments

genome

the query genome sequence. [as FastaSeq]

compare

the comparison genome sequence. [as FastaSeq]

windowsSize

the sliding window size in bp, default 1kb. [as integer]

Details

Authors

comparative_toolkit

Value

profile rows ordered by the site position, an array of WindowDelta

clr value class

Examples

[Package sigma_difference version 1.0.0.0 Index]