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@@ -117,10 +117,10 @@ CALDER_sub_domains(intermediate_data_file,
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| **ref_genome** | One of 'hg19', 'hg38', 'mm9', 'mm10', 'others' (default).
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| **annotation_track** | A table in data.frame or data.table format
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| **contact_file_hic** | Path to the hic
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-| **chrs** | vector of character or numeric. Chromosome names to be analyzed.
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+| **chrs** | chromosome names to be analyzed
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| **bin_size** | numeric, the size of a bin in consistent with the contact table
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-| **dloop** | Find differential loops anchored in at least one of the differential compartments across the samples (Optional but recommended)
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-| **viz** | Generate IGV vizualization HTML file. Must have performed other steps in order (optional ones not strictly necessary) before this one.
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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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| **enrich** | Perform gene enrichment analysis (GSEA) of genes in differential compartments/loops
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Yuanlong LIU