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@@ -119,7 +119,7 @@ CALDER_sub_domains(intermediate_data_file,
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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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-| **bin_size** | numeric, the size of a bin in consistent with the contact table
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+| **bin_size** | the bin_size (resolution) for the analysis. `bin_size` should be consistent with `contact_file_dump` or `contact_tab_dump` when these files were provided as input, otherwise `bin_size` should exist in the `contact_file_hic` file
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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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Yuanlong LIU