genome.delta_star_islands {sigma_difference} R Documentation

The sliding window ``delta*`` profile of the genome against its own global

Description

average genome signature: the alien DNA that has not yet been ameliorated<br /> shows a signature deviating from the host average and therefore appears as<br /> peaks on the curve (e.g. the pathogenicity islands).

Usage

genome.delta_star_islands(genome,
    windowSize = 50000,
    stepSize = 5000);

Arguments

genome

the genome nucleotide sequence. [as FastaSeq]

windowSize

the sliding window size in bp, default = the paper's 50kb contig size. [as integer]

stepSize

the sampling step in bp. [as integer]

Details

Authors

comparative_toolkit

Value

the profile rows ordered by the site position

clr value class

Examples

[Package sigma_difference version 1.0.0.0 Index]