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@@ -114,8 +114,8 @@ CALDER_sub_domains(intermediate_data_file,
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| Parameters | Description |
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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`. 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_dump** |A list of contact files in dump format, named by `chrs`. Each contact file stores the contact information of the corresponding `chr`
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+| **contact_tab_dump** | 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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Yuanlong LIU