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@@ -111,10 +111,19 @@ CALDER_sub_domains(intermediate_data_file,
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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 | Parameters |
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+| Parameters | Description | Examaple |
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| --------------------- | ----------------------- | ----------------------- |
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| **contact_tab_straw** | **contact_tab_straw**
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-
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+| **ref_genome** | One of 'hg19', 'hg38', 'mm9', 'mm10', 'others' (default). |
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+| **annotation_track** | A genomic annotation track in data.frame or data.table format. This track will be used for determing the A/B compartment direction and should presumably have higher values | in A than in B compartment. Some suggested tracks can be:
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+| **contact_file_hic** | Path to the hic
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+| **chrs** | A vector of chromosome names to be analyzed, with or without 'chr'. e.g., `chrs = c(21:22, 'X')` or `chrs = 'chrX'`
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+| **bin_size** | numeric, the size of a bin in consistent with the contact table
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+| **save_dir** | the directory to save outputs
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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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+| **n_cores** | integer. Number of cores to be registered for running CALDER in parallel
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+| **single_binsize_only** | logical. If TRUE, CALDER will compute compartments only using the bin_size specified by the user and not do bin size optimization
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+| **sub_domains** | logical, whether to compute nested sub-domains
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### Output:
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Yuanlong LIU