Elemental formulas (O2 and H2O) are no longer subscripted
in cplab.
Update terminology: stoichiometric oxygen and water content instead of oxidation and hydration state.
The package has been revised to focus on chemical analysis of proteins. Functions have been added for reading FASTA files and calculating more chemical metrics. Data, functions, and vignettes for differential expression analysis have been moved to JMDplots. Amino acid compositions of human proteins are still packaged with canprot.
Add vignettes Demos for canprot and More about metrics.
Add demos ‘thermophiles.R’, ‘locations.R’, and ‘redoxins.R’.
Add add_cld() (adds compact letter display to boxplots),
used in ‘demo/locations.R’.
read_fasta(), count_aa(), and sum_aa() have
been renamed and moved from CHNOSZ to canprot.
calc_metrics() and add_hull() have been moved from
chem16S to canprot and are used in
‘demo/thermophiles.R’.
Add functions for metrics: plength() (protein length),
V0() and S0() (standard molal volume and entropy per
residue), pV0() and pS0() (volume and entropy per protein),
V0g() and S0g() (specific volume and entropy),
Zcg() (specific carbon oxidation state),
nO2g() and nH2Og()
(specific stoichiometric oxidation and hydration state),
Density() (mass density), SV() (entropy density),
HC(), NC(), OC(), and SC() (elemental ratios),
nC() and pnC() (C atoms per residue and per protein),
Cost() (metabolic cost of amino acids from
Akashi and Gojobori, 2002),
RespiratoryCost() and FermentativeCost()
(respiratory and fermentative costs from
Wagner, 2005), and
B20Cost(), Y20Cost(), and H11Cost() (biosynthetic
costs from Zhang et
al., 2018).
Rename ZCAA(), O2AA(), H2OAA(), and
MWAA() to Zc(), nO2(), nH2O(), and
MW().
Add terminal_H2O argument to nH2O(), used to specify
how terminal -H and -OH groups are counted (they are not by default).
Add ... argument to functions to permit using the same
arguments for all metrics in get() or do.call()
constructions.
Objects in cplab are now quote()-ed instead of
expression()s for easier downstream handling.
protcomp() has been renamed human_aa().