Exports genotype tables to various flat file formats.

exportGenotypeTable(
  tasObj,
  file,
  format = c("vcf", "hapmap", "plink", "flapjack", "hdf5"),
  keepDepth = TRUE,
  taxaAnnotations = TRUE,
  branchLengths = TRUE
)

Arguments

tasObj

An object of class TasselGenotypePenotype that contains a genotype table.

file

Output file name.

format

Export file format. This function current supports the following:

  • vcf - A VCF (variant call) file

  • hapmap - HapMap files

  • plink - Plink files

  • flapjack - FlapJack files

  • hdf5 - HDF5 (hierarchical data format v5) files

keepDepth

Whether to keep depth if format supports depth. Defaults to TRUE.

taxaAnnotations

Whether to include taxa annotations if format supports taxa. Defaults to TRUE.

branchLengths

Whether to include branch lengths for Newick formatted files. Defaults to TRUE.