bison {JMDplots}

R Documentation

Relative stabilities of proteins inferred from a hot-spring metagenome

Description

Plots from the papers by Dick and Shock (2011 and 2013).

Usage

  bison1()
  bison2()
  bison3()
  bison4()
  bison5()
  bison6(plot.it = TRUE)
  bison7(equil.results)
  bison8(equil.results)

Arguments

plot.it	logical, make a plot?
equil.results	list, value returned by bison6

Details

This table gives a brief description of each function.

bison1	Measured T and pH
bison2	Carbon oxidation state of proteins
bison3	Chemical affinities (table)
bison4	Relative stabilities along a temperature and chemical gradient
bison5	Comparing old and new methionine sidechain parameters
bison6	Metastable equilibrium model for relative abundances
bison7	Activity of hydrogen comparison
bison8	Comparison of model and observed abundances

Files in extdata/bison

DS11.csv, DS13.csv

These files contain average amino acid compositions of groups of proteins inferred from metagenomic sequences. The groups correspond to proteins with a common functional annotation (DS11) or taxonomic affiliation (DS13). The data are from Dick and Shock, 2011 and 2013.

References

Dick JM and Shock EL (2011) Calculation of the relative chemical stabilities of proteins as a function of temperature and redox chemistry in a hot spring. PLOS One 6, e22782. doi:10.1371/journal.pone.0022782

Dick JM and Shock EL (2013) A metastable equilibrium model for the relative abundance of microbial phyla in a hot spring. PLOS One 8, e72395. doi:10.1371/journal.pone.0072395

Examples

bison1()

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