CHNOSZ (version 1.0.8)

more.aa: Proteins from Model Organisms

Description

Retrieve the amino acid compositions of one or more proteins from Escherichia coli or Saccharomyces cerevisiae.

Usage

more.aa(protein = NULL, organism)

Arguments

protein

character, name of protein

organism

character, name of organism (Eco or Sce)

Value

A data frame, or list of data frames, containing the amino acid composition(s) of the specified protein(s) in the format of thermo$protein.

Details

more.aa retrieves the amino acid composition(s) of the indicated proteins in either Escherichia coli or Saccharomyces cerevisiae. The value of organism can be one of Eco or Sce. The calculation depends on the data files extdata/protein/Eco.csv.xz and extdata/protein/Sce.csv.xz, which contain the amino acid compositions of the proteins. The protein argument should be a vector or a list of vectors of one or more Ordered Locus Names (OLN) or Open Reading Frame (ORF) names that are found in these files. The output data frame contains rows with NA compositions for names that are not matched.

See Also

extdata describes the sources of compositional data for the proteins. Other examples of usage of more.aa are shown for read.expr.

Examples

# the first 13 names in UniProt for "aminotransferase ecoli"
at.ecoli <- c("BIOA", "ARNB", "SERC", "AAT", "TYRB", "ARGD", 
  "ILVE", "ALAA", "ALAC", "YBDL", "AVTA", "GLMS", "PUUE")
# get the amino acid compositions
# note that ALAA and ALAC are not matched
at.aa <- more.aa(at.ecoli, "Eco")
# what are their formulas and oxidation states
protein.formula(at.aa)
ZC(protein.formula(at.aa))