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| **ref_genome** | One of 'hg19', 'hg38', 'mm9', 'mm10', 'others' (default). | High quality compartment calls were generated for 'hg19' (using hic data from GSE63525), 'hg38' (using hic data from https://data.4dnucleome.org/files-processed/4DNFI1UEG1HD/), 'mm9' (using hic data from GSM3959427), 'mm10' (using hic data from http://hicfiles.s3.amazonaws.com/external/bonev/CN_mapq30.hic)
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| **ref_genome** | One of 'hg19', 'hg38', 'mm9', 'mm10', 'others' (default). | High quality compartment calls were generated for 'hg19' (using hic data from GSE63525), 'hg38' (using hic data from https://data.4dnucleome.org/files-processed/4DNFI1UEG1HD/), 'mm9' (using hic data from GSM3959427), 'mm10' (using hic data from http://hicfiles.s3.amazonaws.com/external/bonev/CN_mapq30.hic)
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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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| **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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| **bin_size** | numeric, the size of a bin in consistent with the contact table
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| **bin_size** | numeric, the size of a bin in consistent with the contact table
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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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| **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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