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@@ -156,7 +156,7 @@ 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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- ref_genome=NULL,
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+ genome=NULL,
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feature_track=feature_track,
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save_dir=save_dir,
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save_intermediate_data=FALSE,
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@@ -176,7 +176,7 @@ contact_tab_dump = lapply(contact_file_dump, data.table::fread)
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CALDER(contact_tab_dump=contact_tab_dump,
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chrs=chrs,
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bin_size=10E3,
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- ref_genome='hg19',
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+ genome='hg19',
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save_dir=save_dir,
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save_intermediate_data=FALSE,
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n_cores=2,
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@@ -194,7 +194,7 @@ 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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- ref_genome=NULL,
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+ genome=NULL,
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save_dir=save_dir,
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save_intermediate_data=FALSE,
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n_cores=2,
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@@ -210,7 +210,7 @@ hic_file = 'HMEC_combined_30.hic' ## can be downloaded from https://ftp.ncbi.nlm
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CALDER(contact_file_hic=hic_file,
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chrs=chrs,
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bin_size=10E3,
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- ref_genome='others',
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+ genome='others',
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save_dir=save_dir,
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save_intermediate_data=FALSE,
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n_cores=2,
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@@ -228,8 +228,8 @@ CALDER(contact_file_hic=hic_file,
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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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-| **ref_genome** | One of 'hg19', 'hg38', 'mm9', 'mm10', 'others' (default). These compartments will be used as reference compartments for optimized bin_size selection. If `ref_genome = others`, a `feature_track` should be provided (see below) and no optimized bin_size selection will be performed
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-| **feature_track** | A genomic feature track in `data.frame` or `data.table` format. This track will be used for determing the A/B compartment direction when `ref_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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+| **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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+| **feature_track** | A genomic feature track in `data.frame` or `data.table` format. This track will be used for determing 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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| **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 the `contact_file_hic` file. Recommended `bin_size` is between 10000 to 50000
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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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Yuanlong LIU