protcomp {canprot}R Documentation

Protein Compositions

Description

Get amino acid and chemical compositions of proteins.

Usage

  protcomp(uniprot = NULL, ip = NULL, basis = "AA", aa_file = NULL,
           updates_file = NULL)

Arguments

uniprot

character, UniProt IDs of proteins

ip

numeric, indices of active proteins in CHNOSZ

basis

character, keyword for basis species to use

aa_file

character, file name

updates_file

character, file name

Details

This function retrieves the amino acid compositions of one or more proteins specified by uniprot or ip, then calculates some chemical compositional properties using functions provided by CHNOSZ. basis selects the basis species used for the calculations; use inorganic for CO2, NH3, H2S, H2O, and O2, or AA (the default) for cysteine, glutamic acid, glutamine, H2O, and O2. These two settings correspond to “basis I” and “basis II” as described in Dick, 2016.

This function depends on the amino acid compositions of human proteins, which are made available by data(canprot). If aa_file is specified, additional amino acid compositions to be considered are read from this file, which should be in the same format as e.g. human_extra.csv (see also thermo$protein). If updates_file is specified, these ID mappings are included alongside the packaged uniprot_updates.

Value

The function returns a list with elements protein.formula (elemental compositions of the proteins), ZC (average oxidation state of carbon), protein.basis (compositions of the proteins in terms of the basis species), protein.length (lengths of the amino acid sequences), residue.basis (per-residue compositions of the proteins in terms of the basis species), residue.formula (per-residue elemental compositions of the proteins), and aa (amino acid compositions of the proteins).

References

Dick, J. M. (2016) Proteomic indicators of oxidation and hydration state in colorectal cancer. PeerJ 4, e2238. doi: 10.7717/peerj.2238

Examples

data(canprot)
protcomp("P24298")

[Package canprot version 0.0.2 Index]