alien.genes.scan {sigma_difference} R Documentation

Identify the alien (laterally transferred) genes with the 2D threshold

Description

method (the paper's B. subtilis thresholds by default):<br /><br /> B(g|all) > 0.42 and B(g|RP) > 0.45: alien gene - unlike both the average<br /> host gene and the host highly expressed genes;<br /><br /> B(g|all) > 0.42 but B(g|RP) < 0.45: highly expressed host gene.

Usage

alien.genes.scan(genes,
    rpPattern = "ribosomal protein",
    biasAll = 0.42,
    biasRP = 0.45);

Arguments

genes

all CDS gene sequences of the genome under study. [as FastaFile]

rpPattern

the ribosomal protein product name matching pattern; pass an empty string to skip the B(g|RP) axis. [as string]

biasAll

the B(g|all) threshold, default = paper value 0.42. [as double]

biasRP

the B(g|RP) threshold, default = paper value 0.45. [as double]

Details

Authors

comparative_toolkit

Value

the classification prediction of every long gene

clr value class

Examples

[Package sigma_difference version 1.0.0.0 Index]