Output Handling

Save a both exon and intron counts to an HDF5 file (tome)

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write_tome_data(exon_mat = NULL, intron_mat = NULL,
  tome = "counts.tome", cols_are = "sample_name", overwrite = F,
  orientations = "both", compression_level = 4)

`exon_mat`	The exon matrix to store in dgCMatrix format
`intron_mat`	The intron matrix to store in dgCMatrix format
`tome`	The HDF5 file to write to
`cols_are`	Specifies whether columns in the matrix are sample_ids or genes
`overwrite`	Whether or not to overwrite an existing tome
`orientations`	Which data orientations to write. Options are "both","gene_name", and "sample_name". "gene_name" and "sample_name" refer to the indexing of the matrix (i.e. columns in a dgCMatrix). Usually, you'll want to use the default, "both", to ensure compatibility with scrattch.
`compression_level`	The data compression level for large HDF5 matrix objects. default = 4.