rliger: mergeH5 – R documentation

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mergeH5

Merge hdf5 files

Description

This function merges hdf5 files generated from different libraries (cell ranger by default) before they are preprocessed through Liger pipeline.

Usage

mergeH5(
  file.list,
  library.names,
  new.filename,
  format.type = "10X",
  data.name = NULL,
  indices.name = NULL,
  indptr.name = NULL,
  genes.name = NULL,
  barcodes.name = NULL
)

Arguments

`file.list`	List of path to hdf5 files.
`library.names`	Vector of library names (corresponding to file.list)
`new.filename`	String of new hdf5 file name after merging (default new.h5).
`format.type`	string of HDF5 format (10X CellRanger by default).
`data.name`	Path to the data values stored in HDF5 file.
`indices.name`	Path to the indices of data points stored in HDF5 file.
`indptr.name`	Path to the pointers stored in HDF5 file.
`genes.name`	Path to the gene names stored in HDF5 file.
`barcodes.name`	Path to the barcodes stored in HDF5 file.

Value

Directly generates newly merged hdf5 file.

Examples

## Not run: 
# For instance, we want to merge two datasets saved in HDF5 files (10X CellRanger)
# paths to datasets: "library1.h5","library2.h5"
# dataset names: "lib1", "lib2"
# name for output HDF5 file: "merged.h5"
mergeH5(list("library1.h5","library2.h5"), c("lib1","lib2"), "merged.h5")

## End(Not run)

rliger

Linked Inference of Genomic Experimental Relationships

v1.0.0

GPL-3

Authors

Joshua Welch [aut, ctb], Chao Gao [aut, ctb, cre], Jialin Liu [aut, ctb], Joshua Sodicoff [aut, ctb], Velina Kozareva [aut, ctb], Evan Macosko [aut, ctb], Paul Hoffman [ctb], Ilya Korsunsky [ctb], Robert Lee [ctb]

Initial release

2021-04-18