more.aa(protein = NULL, organism)
thermo$protein
.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.extdata
describes the sources of compositional data for the proteins. Other examples of usage of more.aa
are shown for read.expr
.data(thermo)
# 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))
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