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@@ -282,13 +282,13 @@ save_dir/
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### File description:
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-* The `sub_domains` folder stores the final nested boundaries information
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+* The `sub_domains` folder stores the final nested boundaries
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* The `sub_compartments` folder stores the optimal compartment information, including files:
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| Name | Description |
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| --------------------- | ----------------------- |
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-| **all_sub_compartments.bed** | a .bed file containing the optimal sub-compartment information for all `chrs`, that can be visualized in IGV. Different colors were used to distinguish compartments (at the resolution of 8 sub-compartments)
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-| **all_sub_compartments.tsv** | optimal compartment information stored in tabular text format. Each row represents one 10kb region
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+| **all_sub_compartments.bed** | a .bed file containing the optimal compartments for all `chrs`, that can be visualized in IGV. Different colors were used to distinguish compartments (at the resolution of 8 sub-compartments)
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+| **all_sub_compartments.tsv** | optimal compartments stored in tabular text format. Each row represents one 10kb region
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| **all_sub_compartments.tsv** | optimal compartment information stored in tabular text format. Each row represents one 10kb region
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| **cor_with_ref.ALL.txt** | correlation of compartment rank with the reference compartment rank for each of `bin_sizes`, and the optimimal `bin_size` that is finally selected
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| **cor_with_ref.pdf** | correlation of compartment rank with the reference compartment rank using the optimimal `bin_size`
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@@ -301,7 +301,7 @@ save_dir/
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| Name | Description |
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| --------------------- | ----------------------- |
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| **chrxx_domain_hierachy.tsv** | information of compartment domain and their hierarchical organization. The hierarchical structure is fully represented by `compartment_label`, for example, `B.2.2.2` and `B.2.2.1` are two sub-branches of `B.2.2`. The `pos_end` column specifies all compartment domain borders, except when it is marked as `gap`, which indicates it is the border of a gap chromsome region that has too few contacts and was excluded from the analysis (e.g., due to low mappability, deletion, technique flaw)
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-| **chrxx_sub_compartments.bed** | a .bed file containing the sub-compartment information, that can be visualized in IGV. Different colors were used to distinguish compartments (at the resolution of 8 sub-compartments)
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+| **chrxx_sub_compartments.bed** | a .bed file containing the compartment information, that can be visualized in IGV. Different colors were used to distinguish compartments (at the resolution of 8 sub-compartments)
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| **chrxx_domain_boundaries.bed** | a .bed file containing the chromatin domains boundaries, that can be visualized in IGV
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| **chrxx_nested_boundaries.bed** | a .bed file containing the nested sub-domain boundaries, that can be visualized in IGV
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| **chrxx_intermediate_data.Rds** | an Rds file storing the intermediate_data that can be used to compute nested sub-domains (if CALDER is run in two seperated steps)
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Yuanlong LIU