add.protein {CHNOSZ}

R Documentation

Amino Acid Compositions of Proteins

Description

Functions to get amino acid compositions and add them to protein list for use by other functions.

Usage

  add.protein(aa, as.residue = FALSE)
  seq2aa(sequence, protein = NA)
  aasum(aa, abundance = 1, average = FALSE, protein = NULL, organism = NULL)

Arguments

aa	data frame, amino acid composition in the format of thermo()$protein
as.residue	logical, normalize by protein length?
sequence	character, protein sequence
protein	character, name of protein; numeric, indices of proteins (rownumbers of thermo()$protein)
abundance	numeric, abundances of proteins
average	logical, return the weighted average of amino acid counts?
organism	character, name of organism

Details

A ‘⁠protein⁠’ in CHNOSZ is defined by its identifying information and the amino acid composition, stored in thermo$protein. The names of proteins in CHNOSZ are distinguished from those of other chemical species by having an underscore character ("_") that separates two identifiers, referred to as the protein and organism. An example is ‘⁠LYSC_CHICK⁠’. The purpose of the functions described here is to identify proteins and work with their amino acid compositions. From the amino acid compositions, the thermodynamic properties of the proteins can be estimated by group additivity.

seq2aa returns a data frame of amino acid composition for the provided sequence, in the format of thermo()$protein. In this function, the value of the protein argument is put into the protein column of the result. If there is an underscore (e.g. ‘⁠LYSC_CHICK⁠’), it is used to split the text, and the two parts are put into the protein and organism columns.

Given amino acid compositions returned by seq2aa, add.protein adds them to thermo()$protein for use by other functions in CHNOSZ. The amino acid compositions of proteins in aa with the same name as one in thermo()$protein are replaced. Set as.residue to TRUE to normalize by protein length; each input amino acid composition is divided by the corresponding number of residues, with the result that the sum of amino acid frequencies for each protein is 1.

aasum returns a data frame representing the sum of amino acid compositions in the rows of the input aa data frame. The amino acid compositions are multiplied by the indicated abundance; that argument is recycled to match the number of rows of aa. If average is TRUE the final sum is divided by the number of input compositions. The name used in the output is taken from the first row of aa or from protein and organism if they are specified.

Value

For seq2aa, a data frame of amino acid composition and identifying information for proteins. For add.protein, the rownumbers of thermo()$protein that are added and/or replaced. For aasum, a one-row data frame of amino acid composition and identifying information.

See Also

read.fasta for another way of getting amino acid compositions that can be used with add.protein.

pinfo for protein-level functions (length, chemical formulas, reaction coefficients of basis species).

Examples

# Get the amino acid composition of a protein sequence
# (Human Gastric juice peptide 1)
aa <- seq2aa("LAAGKVEDSD", "GAJU_HUMAN")
# Add the protein to CHNOSZ
ip <- add.protein(aa)
# Calculate the protein length and chemical formula
protein.length(ip) # 10
as.chemical.formula(protein.formula(ip)) # "C41H69N11O18"

# Calculate a formula without using add.protein
aa <- seq2aa("ANLSG", "pentapeptide_test")
as.chemical.formula(protein.formula(aa))

# Sum the amino acid compositions of several poliovirus protein subunits
file <- system.file("extdata/protein/POLG.csv", package = "CHNOSZ")
aa <- read.csv(file, as.is = TRUE)
aasum(aa, protein = "POLG_sum")

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