export: Export data from R

In acidgenomics/pipette: Pipette Biological Data In and Out of R

Export data from R

Description

Export data from R

Usage

export(object, con, ...)

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

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

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

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

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

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

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

## S4 method for signature '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.

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.

Note

Updated 2023-11-08.

See Also

Packages:

• readr.

• data.table.

• rio.

• rtracklayer.

• vroom.

Export functions:

• BiocIO::export().

• data.table::fwrite().

• readr::write_delim().

• rio::export().

• rtracklayer::export().

• vroom::vroom_write().

Examples

counts <- matrix(data = seq_len(100L), nrow = 10)
export(object = counts, con = "counts.csv")

## Clean up.
file.remove("counts.csv")

acidgenomics/pipette documentation built on Jan. 31, 2024, 10:32 p.m.