Published October 26, 2022 | Version 1.1
Dataset Open

Data for LSA analysis

Creators

  • 1. Department of Immunology, Microbiology and Parasitology. Faculty of Science and Technology. University of Basque Country (UPV/EHU). Sarriena S/N. 48940. Leioa, Spain
  • 2. Oceanographic Center of Canary Island, Spanish Institute of Oceanography IEO, Vía Espaldón, Parcela 8, Santa Cruz De Tenerife, 38180, Spain
  • 3. Oeschger Centre for Climate Change Research (OCCR), University of Bern, Hochschulstrasse 4, 3012 Bern, Switzerland

Description

This code is supplementary to the paper "Kinetic modulation of bacterial hydrolases by microbial community structure in coastal waters" by Abad et al.  


It contains the following files: 

0) README.txt: 

  • This README file.

1) Complex saturation kinetics modelling.R: 

  • It contains the code developed for the determination of the kinetic parameters of the extracellular enzymatic activities by fitting the hydrolysis rates to four different kinetic models of increasing complexity using a non-linear least squares regression.

2) LSA functions.R:     

  • It contains the functions implemented in R to perform the Local Similarity analysis.
  • Our specific modifications related to the function LocalSimilarity3 are indicated by the comment "#New: modified function".

3) LSA script.R:     

  • It is an updated version of the code developed by Ruan et al (2006) that has been used to perform the Local Similarity analysis in our study. 
  • The comment "#New: modified function” indicates our specific modifications within the original code.
  • The following modifications were added to the original code: 
    • The calculation of the linear interpolation of missing values (NA’s) using the R package zoo (Zeleis et al 2021).
    • The calculation of the q-values by using the R package qvalue (Storey et al 2022).

NOTE: it is important to set the working directory in the same folder where all the provided files are stored.

Files

README.txt

Files (41.0 kB)

Name Size Download all
md5:b759c17589f5477f90e604fdd4c8396e
8.2 kB Download
md5:18b12b6fb6ade28829122633e788fe56
19.3 kB Download
md5:16b94ab7c0cdc6587468d6b5a0566a2f
11.9 kB Download
md5:b4c47243ae65d41ea22a43694f1bbf70
1.6 kB Preview Download

Additional details

References

  • Ruan et al (2006). Local similarity analysis reveals unique associations among marine bacterioplankton species and environmental factors. doi:10.1093/bioinformatics/btl417
  • Storey et al (2022). qvalue: Q-value estimation for false discovery rate control. R package version 2.28.0, http://github.com/jdstorey/qvalue.
  • Zeileis & Grothendieck (2005). zoo: S3 Infrastructure for Regular and Irregular Time Series. doi:10.18637/jss.v014.i06