Write a GDS object from a tidy data frame

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.

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.

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.

Author

Thierry Gosselin thierrygosselin@icloud.com

Examples

if (FALSE) {
data.gds <- radiator::write_gds(data = "shark.rad")
}