chemlab

Formatted labels for indicating chemical metrics on plots.

Combines taxonomic classifications of high-throughput 16S rRNA
gene sequences with reference proteomes of archaeal and bacterial taxa to
generate amino acid compositions of community reference proteomes. Calculates
chemical metrics including carbon oxidation state ('Zc'), stoichiometric
oxidation and hydration state ('nO2' and 'nH2O'), H/C, N/C, O/C, and S/C
ratios, grand average of hydropathicity ('GRAVY'), isoelectric point ('pI'),
protein length, and average molecular weight of amino acid residues. Uses
precomputed reference proteomes for archaea and bacteria derived from the
Genome Taxonomy Database ('GTDB'). Also includes reference proteomes derived
from the NCBI Reference Sequence ('RefSeq') database and manual mapping from
the 'RDP Classifier' training set to 'RefSeq' taxonomy as described by Dick and
Tan (2023) <doi:10.1007/s00248-022-01988-9>. Processes taxonomic
classifications in 'RDP Classifier' format or OTU tables in 'phyloseq-class'
objects from the Bioconductor package 'phyloseq'.

Jeffrey Dick

chem16S

Chemical Metrics for Microbial Communities

chemlab function

<dl> <dt>varname</dt>
<dd>character, the name of a variable</dd></dl>

Arguments

Formatted labels for chemical metrics — chemlab

<dl>

 <dt>varname</dt>
<dd>character, the name of a variable</dd>

</dl>

chemlab: Formatted labels for chemical metrics

Description

Usage

Value

Arguments

Details

See Also

Examples