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A reproducible comparison between the opm package and the DuctApe suite.

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ductape_vs_opm

A reproducible comparison between the opm package and the DuctApe suite. The comparison is made on the ability of the two programs to extract the curve parameters from PM experiments.

Requirements

  • opm v0.9.1 or later
  • DuctApe v0.14.2 or later
  • sqlite3 (for the zmobilis comparison)

Howto

Open RStudio or enter the R prompt

  • source('opm.R')

From the command line

  • ./prepare

  • ./compare

Details

The comparison is made between those curves having AV >= 3 (AV max 4), according to DuctApe. This is done to minimize the impact of small differences in very low curves, then concentrating the analysis on significative differences.

The difference between two parameters is defined as (Vo - Vd)/Vd, where Vo and Vd are the parameters estimated by opm and DuctApe, respectively.

Z. mobilis dataset

The dataset from Z. mobilis ZM4 is used to understand wether DuctApe and opm can come to similar biological conclusions.

From the zmobilis folder:

  • ./prepare

Open RStudio or enter the R prompt

  • source('opm.R')

Again from the command line

  • ./compare

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A reproducible comparison between the opm package and the DuctApe suite.

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