rliger (version 1.0.0)

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")
# }