Write genomic data

Write genomic data using a format-specific write_*() function. The output format can be supplied explicitly or inferred from an unambiguous filename extension. Call the specialized writer directly when additional control is required. With no output, the historical Parquet-writing and GDS-closing behaviour is retained.

When the object is a CoreArray Genomic Data Structure (GDS) file system, the function close the connection with the GDS file. Before doing so it sets the filters (variants and samples) based on the info found in the file.

Used internally in genometranslator and assigner and might be of interest for users.

Usage

write_genome(
  data,
  output = NULL,
  filename = NULL,
  strata = NULL,
  parallel.core = parallel::detectCores() - 1,
  internal = FALSE,
  write.message = "standard",
  verbose = FALSE
)

Arguments

data: An object in the global environment: tidy genomic dataset or GDS connection file
output: Optional output format. Supported values include gds, genepop, fstat, genind, genlight, gtypes, plink, vcf, and the other formats having a corresponding package write_*() function. Default: output = NULL.
filename: Name of the Arrow/Parquet file written for tabular data. The argument is not used when closing a GDS connection.
strata: Optional strata data passed to writers that support it. Default: strata = NULL.
parallel.core: Number of processor cores passed to writers that support it. Default: parallel.core = parallel::detectCores() - 1.
internal: (optional, logical) This is used inside radiator internal code and it stops from writing the file. Default: internal = FALSE.
write.message: (optional, character) Print a message in the console after writing file. With write.message = NULL, nothing is printed in the console. Default: write.message = "standard". This will print message("File written: ", basename(filename)).
verbose: (optional, logical) verbose = TRUE to be chatty during execution. Default: verbose = FALSE.

Value

A file written in the working directory or nothing if it's a GDS connection file.

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.

Author

Thierry Gosselin thierrygosselin@icloud.com

Examples

if (FALSE) { # \dontrun{
require(SeqArray)
genometranslator::write_genome(data = tidy.data, filename = "data.shark.arrow.parquet")
genometranslator::write_genome(data = gds.object)
} # }