moi_marker: Extracts lineages of samples at a specific marker

In MLMOI: Estimating Frequencies, Prevalence and Multiplicity of Infection

Description

For a specific marker, the function goes from one sample to another and finds lineages with the help of the following functions: corrector_numeric along with decoder_str, corrector_string along with decoder_aminoacid and corrector_string along with decoder_snp. Each of these functions are suitable for a particular type of molecular data.

Usage

moi_marker(
  col_j,
  c_l,
  sam,
  samorder,
  conm,
  cons,
  molecular,
  coding,
  cha_num,
  cha_string,
  ambeguity_code,
  represented_bases,
  aa_1,
  aa_2,
  let_3,
  amino_acid,
  aa_symbol,
  compact,
  codon_s,
  rw_col,
  multsh
)

Arguments

col_j	vector; column vector of a specific marker.
c_l	string; marker label.
sam	numeric vector; vector which its elements specify where a new sample starts.
samorder	a vector which its elements specify where a new sample starts.
conm	numeric; the multiple column identifier. For the data of format multiple columns conm > 1.
cons	numeric; the multiple row identifier. For the data of format multiple rows conm > 1.
molecular	string; type of molecular data.
coding	string; coding class of the molecular marker.
cha_num	string vector; vector of symbols (used for microsatellite data).
cha_string	string vector; vector of symbols (used for snp and amino acid).
ambeguity_code	string vector; ambeguity codes for snp data.
represented_bases	string vector; represented bases for those ambeguity codes.
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.
compact	string vector; vector of different codons in compact form.
codon_s	string vector; vector of different codons.
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 with the following elements: 1) a list with elements containing lineages for a specific sample on a specific marker. The order in which samples are entered in dataset is preserved in the list. The lineages are free from typos and are transformed to pre-specified coding class, 2) an identifier whose value is 1 if a warning takes place.

See Also

For further details, please see the following functions: moimport

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