exportGenotypeTable: Export Genotype Table to Disk
In maize-genetics/rTASSEL: R Front-End for TASSEL

exportGenotypeTable

R Documentation

Export Genotype Table to Disk

Description

Exports genotype tables to various flat file formats.

Usage

exportGenotypeTable(
  tasObj,
  file,
  format = c("vcf", "hapmap", "plink", "flapjack"),
  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
`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`.