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@@ -114,10 +114,11 @@ CALDER_sub_domains(intermediate_data_file,
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| Parameters | 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_straw** |A list of contact files in dump format, named by `chrs`
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-| **contact_tab_straw** | xx |xx
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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_straw** |A list of contact files in dump format, named by `chrs`. Each contact file stores the contact information of the named chromosome
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+| **contact_tab_straw** | A list of contact table in dump format, named by `chrs`, stored as an R object
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+| **contact_file_hic** | A hic file generated by Juicer tools. It should contain all chromosomes in `chrs`
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+| **ref_genome** | One of 'hg19', 'hg38', 'mm9', 'mm10', 'others' (default). | When ``
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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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| **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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Yuanlong LIU