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@@ -114,12 +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_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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+| **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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+| **contact_tab_dump** | A list of contact table in dump format, named by `chrs`, stored as an R object. Only one of `contact_file_dump`, `contact_tab_dump`, `contact_file_hic` should be provided
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+| **contact_file_hic** | A hic file generated by Juicer tools. It should contain all chromosomes in `chrs`. Only one of `contact_file_dump`, `contact_tab_dump`, `contact_file_hic` should be provided
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| **ref_genome** | One of 'hg19', 'hg38', 'mm9', 'mm10', 'others' (default). High quality compartment calls were generated for 'hg19' (hic data from GSE63525), 'hg38' (hic data from https://data.4dnucleome.org/files-processed/4DNFI1UEG1HD/), 'mm9' (hic data from GSM3959427), 'mm10' (hic data from http://hicfiles.s3.amazonaws.com/external/bonev/CN_mapq30.hic). These compartments will be used as reference compartments for optimized bin_size selection. If `ref_genome = others`, an `annotation_track` should be provided (see below) and no optimized bin_size selection will be performed
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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 when `ref_genome=others` and should presumably have higher values in A than in B compartment. Some suggested tracks can be gene density, H3K27ac, H3K4me1, H3K4me2, H3K4me3, H3K36me3 (or negative transform of H3K9me3 signals)
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-| **contact_file_hic** | Path to the hic xx
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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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Yuanlong LIU