decoder_aminoacid: Translates the standard ambiguity codes for nucleotides...

In MLMOI: Estimating Frequencies, Prevalence and Multiplicity of Infection

Description

Translates the standard ambiguity codes for nucleotides in amino acid forms from a pre-specified coding class to 3-letter designation of amino acids.

Usage

decoder_aminoacid(
  y,
  c_l,
  r_w,
  aa_1,
  aa_2,
  let_3,
  amino_acid,
  aa_symbol,
  coding,
  rw_col,
  multsh
)

Arguments

y	numeric vector; entries in a cell corresponding to a specific sample and a specific marker.
c_l	string; marker label.
r_w	numeric; sample ID's row number in the excel file.
aa_1	string vector; vector of different amino acids.
aa_2	string vector; vector of different codons.
let_3	string vector; vector of amino acids in 3 letter designation.
amino_acid	string vector; vector of amino acids in full name.
aa_symbol	string vector; vector of amino acids in one letter designation.
coding	string; coding class of the molecular marker.
rw_col	string vector; variable used to switch between row and column in case of transposed data. Namely, c("rows ", "row ", "column ", "columns ").
multsh	string; reports warnings for multiple worksheet datasets.

Value

a list of two elements: 1) a vector of 3-letter designation of amino acids on a marker corresponding to a sample in pre-specified coding class. 2) an identifier whose value is 1 if a warning takes place.

See Also

For further details see: moimport, moi_marker and corrector_string. See also the vignette 'StandardAmbiguityCodes'.

MLMOI documentation built on Jan. 11, 2020, 9:22 a.m.