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Read Genotype Data from R Matrix

Source: R/utils_genotype.R
readNumericGenotypeFromRMatrix.Rd

This function constructs a `TasselNumericGenotype` object from an R matrix by interfacing with the TASSEL Java API. It creates taxa lists, position lists, reference probabilities, and a genotype table using the provided matrix data.

Usage

readNumericGenotypeFromRMatrix(m, asTGP = TRUE)

Arguments

m

A numeric matrix where rows represent taxa and columns represent positions/sites. The matrix values are used to calculate reference probabilities.

asTGP

Should the return object be a "classic" TasselGenotypePhenotype object (TRUE) or should it return a TasselNumericGenotype object (FALSE)? Defaults to TRUE.

Value

An object of class `TasselNumericGenotype` containing the genotype data and metadata.

Details

The following components are constructed using respective Java builder classes:

  • Taxa list is created using the TASSEL_JVM$TAXA_LIST_BUILDER Java class.

  • Position list is constructed using the TASSEL_JVM$POSITION_LIST_BUILDER and TASSEL_JVM$GENERAL_POSITION_BUILDER Java classes.

  • Reference probabilities are built using the TASSEL_JVM$REF_PROBABILITY_BUILDER Java class.

  • The genotype table is created using the TASSEL_JVM$GENOTYPE_TABLE_BUILDER Java class.