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@@ -117,7 +117,7 @@ CALDER_sub_domains(intermediate_data_file,
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| **ref_genome** | One of 'hg19', 'hg38', 'mm9', 'mm10', 'others' (default).
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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 and should presumably have higher values in A than in B compartment. Some suggested tracks can be:
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| **contact_file_hic** | Path to the hic
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-| **chrs** | chromosome names to be analyzed
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+| **chrs** | A vector of chromosome names to be analyzed, with or without 'chr'. e.g., `chrs = c(21:22, 'X')` or `chrs = 'chrX'`
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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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@@ -148,7 +148,7 @@ CALDER_sub_domains(intermediate_data_file,
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## Output Structure
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-The output of the workflow is stored in the folder specified by `--out_dir` ("results" by default) and will look like this:
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+The output of the workflow is stored in the folder specified by `--save_dir` ("results" by default) and will look like this:
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```
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results/
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└── HiC_sample_1
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Yuanlong LIU