exportGenotypeTable: Export Genotype Table to Disk

View source: R/utilities_export.R

exportGenotypeTableR 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.


maize-genetics/rTASSEL documentation built on Nov. 13, 2023, 7:18 a.m.