Export

Export data out of R and write to disk.

export(object, ...)

# S4 method for character
export(
  object,
  ext = "txt",
  dir = getOption("acid.export.dir", default = "."),
  file = NULL,
  append = FALSE,
  overwrite = getOption("acid.overwrite", default = TRUE),
  quiet = getOption("acid.quiet", default = FALSE)
)

# S4 method for matrix
export(
  object,
  ext = getOption("acid.export.ext", default = "csv"),
  dir = getOption("acid.export.dir", default = "."),
  file = NULL,
  rownames = TRUE,
  colnames = TRUE,
  overwrite = getOption("acid.overwrite", default = TRUE),
  quiet = getOption("acid.quiet", default = FALSE)
)

# S4 method for data.frame
export(
  object,
  ext = getOption("acid.export.ext", default = "csv"),
  dir = getOption("acid.export.dir", default = "."),
  file = NULL,
  rownames = TRUE,
  colnames = TRUE,
  overwrite = getOption("acid.overwrite", default = TRUE),
  quiet = getOption("acid.quiet", default = FALSE)
)

# S4 method for DataFrame
export(
  object,
  ext = getOption("acid.export.ext", default = "csv"),
  dir = getOption("acid.export.dir", default = "."),
  file = NULL,
  rownames = TRUE,
  colnames = TRUE,
  overwrite = getOption("acid.overwrite", default = TRUE),
  quiet = getOption("acid.quiet", default = FALSE)
)

# S4 method for Matrix
export(
  object,
  ext = "mtx",
  dir = getOption("acid.export.dir", default = "."),
  file = NULL,
  overwrite = getOption("acid.overwrite", default = TRUE),
  quiet = getOption("acid.quiet", default = FALSE)
)

# S4 method for GenomicRanges
export(
  object,
  ext = getOption("acid.export.ext", default = "csv"),
  dir = getOption("acid.export.dir", default = "."),
  file = NULL,
  rownames = TRUE,
  colnames = TRUE,
  overwrite = getOption("acid.overwrite", default = TRUE),
  quiet = getOption("acid.quiet", default = FALSE)
)

Arguments

object	Object. An object supporting `dim()`, or a supported class capable of being coerced to `data.frame`, to be written to disk.
ext	`character(1)`. Output file format extension. `matrix` supported arguments: Comma separated values (CSV): `"csv"`, `"csv.bz2"`, `"csv.gz"`, `"csv.xz"`, `"csv.zip"`. Tab separated values (TSV): `"tsv"`, `"tsv.bz2"`, `"tsv.gz"`, `"tsv.xz"`, `"tsv.zip"`. `Matrix` (`sparseMatrix`) supported arguments: MatrixMarket exchange (MTX): `"mtx"`, `"mtx.bz2"`, `"mtx.gz"`, `"mtx.xz"`, `"mtx.zip"`.
dir	`character(1)`. Directory path.
file	`character(1)`. File path. When left unset (default), the `ext` and `dir` arguments will be used instead.
append	`logical(1)`. Append to output file. When enabled, automatically sets `overwrite` argument to `FALSE`. Requires readr package to be installed.
overwrite	`logical(1)`. Overwrite existing file on disk.
quiet	`logical(1)`. Perform command quietly, suppressing messages.
rownames	`logical(1)`. Apply to row names.
colnames	`logical(1)`. Apply to column names.
...	Additional arguments.

Value

Invisible character. File path(s).

Note

Updated 2021-03-16.

Row names

Some export utilities in R have a tendency to drop row names when writing to disk in CSV format. For example, the readr family of functions never write row names by design. This is a really poor default setting for handling genomic data, which often contain gene identifiers in the row names. Here we're performing any internal tibble coercion step to ensure row names are always moved to a "rowname" column in the CSV export.

Debugging

Note that this function currently wraps data.table::fwrite() by default for exporting data.frame and matrix class objects.

Examples