This function will generate an object of SummarizedExperiment class for marker data derived from a TasselGenotypePhenotype class object.

getSumExpFromGenotypeTable(
  tasObj,
  useRef = FALSE,
  coerceDosageToInt = TRUE,
  verbose = FALSE
)

Arguments

tasObj

An object of class TasselGenotypePenotype.

useRef

Use reference alleles or major alleles at sites. If FALSE, major alleles will be used. Defaults to FALSE.

coerceDosageToInt

Should dosage array be returned as integer values? If FALSE, dosage array will be returned as type raw byte values. Returning raw byte values. Will greatly save on memory. Defaults to TRUE.

verbose

Should messages be displayed to console? Defaults to FALSE.

Value

Returns a SummarizedExperiment of TASSEL genotype data.