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@@ -214,12 +214,12 @@ CALDER(contact_file_dump=contact_file_dump,
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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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| **genome** | One of 'hg19', 'hg38', 'mm9', 'mm10', 'others' (default). These compartments will be used as reference compartments for optimized bin_size selection. If `genome = others`, a `feature_track` should be provided (see below) and no optimized bin_size selection will be performed
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-| **feature_track** | A genomic feature track in `data.frame` or `data.table` format. This track will be used for determing the A/B compartment direction when `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** | The bin_size (resolution) to run CALDER. `bin_size` should be consistent with the data resolution in `contact_file_dump` or `contact_tab_dump` if these files are provided as input, otherwise `bin_size` should exist in `contact_file_hic`. Recommended `bin_size` is between **10000 to 100000**
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| **save_dir** | the directory to be created for saving outputs
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+| **bin_size** | The bin_size (resolution) to run CALDER. `bin_size` should be consistent with the data resolution in `contact_file_dump` or `contact_tab_dump` if these files are provided as input, otherwise `bin_size` should exist in `contact_file_hic`. Recommended `bin_size` is between **10000 to 100000**
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+| **single_binsize_only** | logical. If TRUE, CALDER will compute compartments only using the bin_size specified by the user and not do bin size optimization
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+| **feature_track** | A genomic feature track in `data.frame` or `data.table` format. This track will be used for determing the A/B compartment direction when `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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| **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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-| **single_binsize_only** | logical. If TRUE, CALDER will compute compartments only using the bin_size specified by the user and not do bin size optimization
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| **sub_domains** | logical, whether to compute nested sub-domains
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Yuanlong LIU