MLMOI (version 0.1.2)

decoder_snp: Converts ambeguity codes to represented bases

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
)

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.

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.

See Also

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