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@@ -201,7 +201,7 @@ names(contact_file_dump) = chrs
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CALDER(contact_file_dump=contact_file_dump,
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chrs=chrs,
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bin_size=10E3,
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- genome=others,
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+ genome='others',
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save_dir=save_dir,
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feature_track=feature_track,
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save_intermediate_data=FALSE,
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@@ -219,7 +219,7 @@ CALDER(contact_file_dump=contact_file_dump,
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| **contact_file_dump** |A list of contact files in dump format, named by `chrs`. Each contact file stores the contact information of the corresponding `chr`. Only one of `contact_file_dump`, `contact_tab_dump`, `contact_file_hic` should be provided
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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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+| **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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| **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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Yuanlong LIU