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@@ -223,7 +223,7 @@ CALDER(contact_file_dump=contact_file_dump,
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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 determining 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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+| **feature_track** | A genomic feature track in `data.frame` or `data.table` format with 4 columns (chr, start, end, score). This track will be used for determining 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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| **sub_domains** | logical, whether to compute nested sub-domains
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Yuanlong LIU