decoder_snp: Converts ambeguity codes to represented bases

In MLMOI: Estimating Frequencies, Prevalence and Multiplicity of Infection

Description

Translates the nucleotide ambiguity codes as defined in DNA Sequence Assembler from a pre-specified coding class to 4-letter codes.

Usage

decoder_snp(
  y,
  c_l,
  r_w,
  ambeguity_code,
  represented_bases,
  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.
ambeguity_code	string vector; ambeguity codes for snp data.
represented_bases	string vector; represented bases for those ambeguity codes.
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 represented bases 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.