write_gds: Write a GDS object from a tidy data frame

In thierrygosselin/radiator: RADseq Data Exploration, Manipulation and Visualization using R

Write a GDS object from a tidy data frame

Description

Write a Genomic Data Structure (GDS) file format gdsfmt and object of class SeqVarGDSClass from a tidy data frame.

Used internally in radiator and might be of interest for users.

Usage

write_gds(
  data,
  data.source = NULL,
  filename = NULL,
  open = TRUE,
  verbose = TRUE
)

Arguments

data	A tidy data frame object in the global environment or a tidy data frame in wide or long format in the working directory. How to get a tidy data frame ? Look into radiator tidy_genomic_data.
data.source	(optional, character) The name of the software that generated the data. e.g. data.source = "Stacks v.2.4". Default: data.source = NULL.
filename	(optional) The file name of the Genomic Data Structure (GDS) file. radiator will append .gds.rad to the filename. If filename chosen is already present in the working directory, the default radiator_datetime.gds.rad is chosen. Default: filename = NULL.
open	(optional, logical) Open or not the radiator connection. Default: open = TRUE.
verbose	(optional, logical) When verbose = TRUE the function is a little more chatty during execution. Default: verbose = TRUE.

Value

An object in the global environment of class SeqVarGDSClass and a file in the working directory.

Author(s)

Thierry Gosselin [e-mail]

References

Zheng X, Levine D, Shen J, Gogarten SM, Laurie C, Weir BS. A high-performance computing toolset for relatedness and principal component analysis of SNP data. Bioinformatics. 2012;28: 3326-3328. doi:10.1093/bioinformatics/bts606

Zheng X, Gogarten S, Lawrence M, Stilp A, Conomos M, Weir BS, Laurie C, Levine D (2017). SeqArray – A storage-efficient high-performance data format for WGS variant calls. Bioinformatics.

Examples

## Not run: 
data.gds <- radiator::write_gds(data = "shark.rad")

## End(Not run)

thierrygosselin/radiator documentation built on Nov. 7, 2024, 1:30 p.m.