pre.processing

Data table including the confirmed operon pairs (OPs). See <code>select.ops</code>.

Data table including gene pairs with an operon status to (re)define (POPs). See <code>select.pops</code>.

POPs

Data table including the operon pairs annotated in DOOR database (DOPs). See <code>select.ops.indoor</code>.

DOPs

Charcater vector indicating the method to use for the normalization step. Default value is "n0".

type

verbose

Data table including the confirmed non-operon pairs (NOPs). See <code>select.nops</code>.


n0 - without normalization
n1 - standardization ((x-mean)/sd)
n2 - positional standardization ((x-median)/mad)
n3 - unitization ((x-mean)/range)
n4 - unitization with zero minimum ((x-min)/range)
n5 - normalization in range &lt;-1,1> ((x-mean)/max(abs(x-mean)))


internal

An implementation of the computational strategy for the
comprehensive analysis of condition-dependent operon maps in prokaryotes
proposed by Fortino et al. (2014) <DOI:10.1186/1471-2105-15-145>.
It uses RNA-seq transcriptome profiles to improve prokaryotic operon map inference.

pre.processing: Normalize the data before the classification step.

Description

Usage

Arguments