rliger (version 2.0.1)

writeH5: Write in-memory data into H5 file

Description

This function writes in-memory data into H5 file by default in 10x cellranger HDF5 output format. The main goal of this function is to allow users to integrate large H5-based dataset, that cannot be fully loaded into memory, with other data already loaded in memory using runOnlineINMF. In this case, users can write the smaller in-memory data to H5 file instead of loading subset of the large H5-based dataset into memory, where information might be lost.

Basing on the goal of the whole workflow, the data will always be written in a CSC matrix format and colnames/rownames are always required.

The default method coerces the input to a dgCMatrix. Methods for other container classes tries to extract proper data and calls the default method.

Usage

writeH5(x, file, ...)
# S3 method for default
writeH5(x, file, ...)
# S3 method for dgCMatrix
writeH5(
  x,
  file,
  overwrite = FALSE,
  indicesPath = "matrix/indices",
  indptrPath = "matrix/indptr",
  dataPath = "matrix/data",
  shapePath = "matrix/shape",
  barcodesPath = "matrix/barcodes",
  featuresPath = "matrix/features/name",
  ...
)
# S3 method for ligerDataset
writeH5(x, file, ...)
# S3 method for liger
writeH5(x, file, useDatasets, ...)

Value

Nothing is returned. H5 file will be created on disk.

Arguments

x

An object with in-memory data to be written into H5 file.

file

A character string of the file path to be written.

...

Arguments passed to other S3 methods.

overwrite

Logical, whether to overwrite the file if it already exists. Default FALSE.

indicesPath, indptrPath, dataPath

The paths inside the H5 file where the dgCMatrix constructor i, p, and x will be written to, respectively. Default using cellranger convention "matrix/indices", "matrix/indptr", and "matrix/data".

shapePath

The path inside the H5 file where the shape of the matrix will be written to. Default "matrix/shape".

barcodesPath

The path inside the H5 file where the barcodes/colnames will be written to. Default "matrix/barcodes". Skipped if the object does not have colnames.

featuresPath

The path inside the H5 file where the features/rownames will be written to. Default "matrix/features/name". Skipped if the object does not have rownames.

useDatasets

For liger method. Names or indices of datasets to be written to H5 files. Required.

See Also

10X cellranger H5 matrix detail

Examples

raw <- rawData(pbmc, "ctrl")
writeH5(raw, tempfile(pattern = "ctrl_", fileext = ".h5"))