Write tidy genomic data file or close GDS file

When datasets are a tidy data frame, the function provides a fast way to write a .arrow.parquet file. It superseded the .rad file format that is essentially the .fst format provided by the the package fst. The .fst end was replaced by .rad to remove the confusion with population genetics statistic fst ... The decision to use arrow parquet format from Apache was taken because the package is easier to install than fst, write and read files faster and files sizes are are also smaller. When the object is a CoreArray Genomic Data Structure (GDS) file system, the function set filters (variants and samples) based on the info found in the file and close the connection with the GDS file.

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

write_rad(
  data,
  path = NULL,
  filename = NULL,
  tsv = FALSE,
  internal = FALSE,
  append = FALSE,
  col.names = TRUE,
  write.message = "standard",
  verbose = FALSE
)

Arguments

data

An object in the global environment: tidy data frame or GDS connection file

path

(optional) For tidy data frame, the path to write the data on disk. Default: path = NULL.

filename

(optional) Name of the file (when using tsv files). Default: filename = NULL.

tsv

(optinal, logical) To trigger saving using readr::write_tsv. Default: tsv = FALSE.

internal

(optional, logical) This is used inside radiator internal code and it stops from writting the file. Default: internal = FALSE.

append

(optional, logical) If FALSE, will overwrite existing file. If TRUE, will append to existing file. In both cases, if file does not exist a new file is created. Default: append = FALSE.

col.names

(optional, logical) Write columns names at the top of the file? Must be either TRUE or FALSE. Default: col.names = TRUE.

write.message

(optional, character) Print a message in the console after writting file. With write.message = NULL, nothing is printed in the console. Default: write.message = "standard". This will print message("File written: ", folder_short(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.

See also

fst GDS read_rad

Author

Thierry Gosselin thierrygosselin@icloud.com

Examples

if (FALSE) { # \dontrun{
require(SeqArray)
radiator::write_rad(data = tidy.data, path = "data.shark.rad")
radiator::write_rad(data = gds.object)
} # }