hdf5_import

HDF5MATRIX_CORE

1 Description

Modern wrapper for importing CSV, TSV, or other delimited text files into HDF5 format. Returns an HDF5Matrix object ready for use.

2 Usage

hdf5_import(...)

3 Arguments

Parameter	Description
`source`	Character. Path to local file or URL to import. Supports compressed files (.gz, .tar.gz, .zip, .bz2).
`filename`	Character. Path to HDF5 output file (created if doesn’t exist).
`dataset`	Character. Full dataset path (e.g., “data/imported” or “group/dataset”).
`sep`	Character. Field separator. Default (auto-detect from extension: “,” for .csv, “\t” for .tsv, “\t” otherwise).
`header`	Logical or character vector. If , first row contains column names. If character vector, use these as column names. Default .
`rownames`	Logical or character vector. If , first column contains row names. If character vector, use these as row names. Default .
`overwrite`	Logical. If , overwrite dataset if exists. Default .
`parallel`	Logical. Use parallel processing for import. Default .
`threads`	Integer. Number of threads for parallel processing. Default (uses all available cores).

4 Value

object pointing to the imported data.

5 Details

This function is a modern, user-friendly wrapper around bdImportData_hdf5 and bdImportTextFile_hdf5. It:

Supported formats:

Memory efficiency: Import is done in a streaming fashion, so very large files can be imported without loading them entirely into memory.

6 Examples

\donttest{
csv_file  <- tempfile(fileext = ".csv")
hdf5_file <- tempfile(fileext = ".h5")

# Write sample numeric data
write.table(matrix(rnorm(50), nrow = 10, ncol = 5),
            csv_file, sep = ",", row.names = FALSE, col.names = TRUE)

# Import CSV to HDF5
mat <- hdf5_import(
  source   = csv_file,
  filename = hdf5_file,
  dataset  = "raw/data",
  sep      = ","
)
dim(mat)

hdf5_close_all()
unlink(c(csv_file, hdf5_file))
}

7 See Also

bdImportData_hdf5 for the underlying implementation, hdf5_create_matrix for creating matrices from R objects

--- title: "hdf5_import" subtitle: "hdf5_import" --- <span class="category-badge hdf5matrix_core">HDF5MATRIX_CORE</span> ## Description Modern wrapper for importing CSV, TSV, or other delimited text files into HDF5 format. Returns an `HDF5Matrix` object ready for use. ## Usage ```r hdf5_import(...) ``` ## Arguments ::: {.param-table} | Parameter | Description | |-----------|-------------| | `source` | Character. Path to local file or URL to import. Supports compressed files (.gz, .tar.gz, .zip, .bz2). | | `filename` | Character. Path to HDF5 output file (created if doesn't exist). | | `dataset` | Character. Full dataset path (e.g., "data/imported" or "group/dataset"). | | `sep` | Character. Field separator. Default \code{NULL} (auto-detect from extension: "," for .csv, "\\t" for .tsv, "\\t" otherwise). | | `header` | Logical or character vector. If \code{TRUE}, first row contains column names. If character vector, use these as column names. Default \code{TRUE}. | | `rownames` | Logical or character vector. If \code{TRUE}, first column contains row names. If character vector, use these as row names. Default \code{FALSE}. | | `overwrite` | Logical. If \code{TRUE}, overwrite dataset if exists. Default \code{FALSE}. | | `parallel` | Logical. Use parallel processing for import. Default \code{TRUE}. | | `threads` | Integer. Number of threads for parallel processing. Default \code{NULL} (uses all available cores). | ::: ## Value ::: {.return-value} \code{HDF5Matrix} object pointing to the imported data. ::: ## Details This function is a modern, user-friendly wrapper around [bdImportData_hdf5](../hdf5_io_management/bdImportData_hdf5.html) and [bdImportTextFile_hdf5](../hdf5_io_management/bdImportTextFile_hdf5.html). It: \itemize{ \item Automatically detects file format from extension \item Handles compressed files (.gz, .tar.gz, .zip) \item Downloads from URLs automatically \item Returns ready-to-use `HDF5Matrix` object \item Uses sensible defaults for most use cases } **Supported formats:** \itemize{ \item CSV files (.csv) - comma-separated \item TSV files (.tsv, .txt) - tab-separated \item Compressed files (.gz, .tar.gz, .zip, .bz2) \item Remote files (http://, https://, ftp://) } **Memory efficiency:** Import is done in a streaming fashion, so very large files can be imported without loading them entirely into memory. ## Examples ```{r} #| eval: false #| warning: false \donttest{ csv_file <- tempfile(fileext = ".csv") hdf5_file <- tempfile(fileext = ".h5") # Write sample numeric data write.table(matrix(rnorm(50), nrow = 10, ncol = 5), csv_file, sep = ",", row.names = FALSE, col.names = TRUE) # Import CSV to HDF5 mat <- hdf5_import( source = csv_file, filename = hdf5_file, dataset = "raw/data", sep = "," ) dim(mat) hdf5_close_all() unlink(c(csv_file, hdf5_file)) } ``` ## See Also ::: {.see-also} [bdImportData_hdf5](../hdf5_io_management/bdImportData_hdf5.html) for the underlying implementation, [hdf5_create_matrix](hdf5_create_matrix.html) for creating matrices from R objects :::