Create Summarized Experiment from a TASSEL Genotype Table — getSumExpFromGenotypeTable • rTASSEL

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.

Returns a SummarizedExperiment of TASSEL genotype data.