human_aa

Get amino acid compositions of human proteins from their UniProt IDs.

Chemical analysis of proteins based on their amino acid
compositions. Amino acid compositions can be read from FASTA files and used to
calculate chemical metrics including carbon oxidation state and stoichiometric
hydration state, as described in Dick et al. (2020) <doi:10.5194/bg-17-6145-2020>.
Other properties that can be calculated include protein length, grand average of
hydropathy (GRAVY), isoelectric point (pI), molecular weight (MW), standard
molal volume (V0), and metabolic costs (Akashi and Gojobori, 2002
<doi:10.1073/pnas.062526999>; Wagner, 2005 <doi:10.1093/molbev/msi126>;
Zhang et al., 2018 <doi:10.1038/s41467-018-06461-1>). A database of amino acid
compositions of human proteins derived from UniProt is provided.

Jeffrey Dick

canprot

Chemical Analysis of Proteins

human_aa function

<dl> <dt>uniprot</dt>
<dd>character, UniProt IDs of proteins</dd> <dt>aa_file</dt>
<dd>character, file name</dd> <dt>stop_if_missing</dt>
<dd>logical, stop with an error if there are UniProt IDs that can't be found?</dd> <dt>warn_if_duplicated</dt>
<dd>logical, emit a warning if duplicate UniProt IDs are detected?</dd></dl>

Arguments

Get amino acid compositions of human proteins — human_aa

<dl>

 <dt>uniprot</dt>
<dd>character, UniProt IDs of proteins</dd>

 <dt>aa_file</dt>
<dd>character, file name</dd>

 <dt>stop_if_missing</dt>
<dd>logical, stop with an error if there are UniProt IDs that can't be found?</dd>

 <dt>warn_if_duplicated</dt>
<dd>logical, emit a warning if duplicate UniProt IDs are detected?</dd>

</dl>

human_aa: Get amino acid compositions of human proteins

Description

Usage

Value

Arguments

Details

Examples