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Write a GDS object from a tidy data frame

Source: R/gds.R
write_gds.Rd

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

Used internally in genometranslator 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 genometranslator tidy_genome.

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.

Value

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

Data filtering

This writer does not silently filter markers or individuals. It may validate requirements imposed by the destination format and stop with an informative error when the input is unsuitable. It is the user's responsibility to filter and quality-control the data appropriately for the intended analysis before generating the output. Use radr or another suitable workflow when filtering is required.

Dependencies

Required package dependencies are declared in DESCRIPTION and are installed with genometranslator. Any additional dependency needed only for this format or option is identified in this help page. Use genometranslator_dependencies() to inspect the availability of core packages, optional packages, and external executables.

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) { # \dontrun{
data.gds <- genometranslator::write_gds(data = "shark.rad")
} # }