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@@ -123,15 +123,7 @@ CALDER_sub_domains(intermediate_data_file,
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### Paramters:
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-* `contact_mat_file`: path to the contact table of a chromosome
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-* `chr`: chromosome number. Either numeric or character, will be pasted to the output name
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-* `bin_size`: numeric, the size of a bin in consistent with the contact table
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-* `out_dir`: the output directory
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-* `sub_domains`: logical, whether to compute nested sub-domains
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-* `save_intermediate_data`: logical. If TRUE, an intermediate_data will be saved. This file can be used for computing nested sub-domains later on
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-* `genome`: string. Specifies the genome assembly (Default="hg19").
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-| Parameters | Description |
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+| Name | Description |
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| --------------------- | ----------------------- |
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| **chrs** | A vector of chromosome names to be analyzed, with or without 'chr'
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| **contact_file_dump** |A list of contact files in dump format, named by `chrs`. Each contact file stores the contact information of the corresponding `chr`. Only one of `contact_file_dump`, `contact_tab_dump`, `contact_file_hic` should be provided
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Yuanlong LIU