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Export data from R

Source: R/AllGenerics.R, R/export-methods.R
export.Rd

Export data from R

Usage

export(object, con, ...)

# S4 method for DFrame,character
export(
  object,
  con,
  rownames = TRUE,
  colnames = TRUE,
  quote = TRUE,
  overwrite = TRUE,
  engine = c("base", "data.table", "readr"),
  quiet = FALSE
)

# S4 method for GRanges,character
export(
  object,
  con,
  rownames = TRUE,
  colnames = TRUE,
  quote = TRUE,
  overwrite = TRUE,
  engine = c("base", "data.table", "readr"),
  quiet = FALSE
)

# S4 method for List,character
export(object, con, overwrite = TRUE, quiet = FALSE)

# S4 method for Matrix,character
export(object, con, overwrite = TRUE, quiet = FALSE)

# S4 method for atomic,character
export(
  object,
  con,
  append = FALSE,
  overwrite = TRUE,
  engine = c("base", "data.table", "readr"),
  quiet = FALSE
)

# S4 method for data.frame,character
export(
  object,
  con,
  rownames = TRUE,
  colnames = TRUE,
  quote = TRUE,
  overwrite = TRUE,
  engine = c("base", "data.table", "readr"),
  quiet = FALSE
)

# S4 method for list,character
export(object, con, overwrite = TRUE, quiet = FALSE)

# S4 method for matrix,character
export(
  object,
  con,
  rownames = TRUE,
  colnames = TRUE,
  quote = TRUE,
  overwrite = TRUE,
  engine = c("base", "data.table", "readr"),
  quiet = FALSE
)

# S4 method for ANY,missing
export(object, con, ...)

Arguments

object

Object.

con

character(1) or connection. Data connection. Use character(1) to represent a file path.

rownames

logical(1). Apply to row names.

colnames

logical(1). Apply to column names.

quote

logical(1). Surround any character or factor columns by double quotes. Recommended by default.

overwrite

logical(1). Overwrite existing file on disk.

engine

character(1). Engine (package) to use for export.

Currently supported:

  • base

  • data.table

  • readr

quiet

logical(1). Perform command quietly, suppressing messages.

append

logical(1). Append to output file. When enabled, automatically sets overwrite argument to FALSE. Requires readr package to be installed.

...

Additional arguments.

Value

Invisible character or list of file paths.

Note

Updated 2023-11-08.

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".

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 readr::write_delim() by default for exporting DFrame, data.frame, and matrix class objects.

See also

Packages:

Export functions:

Examples

counts <- matrix(data = seq_len(100L), nrow = 10)
export(object = counts, con = "counts.csv")
#> → Exporting counts.csv using base::`write.table()`.

## Clean up.
file.remove("counts.csv")
#> [1] TRUE