|
|
@@ -117,8 +117,8 @@ CALDER_sub_domains(intermediate_data_file,
|
|
|
| **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`
|
|
|
| **contact_tab_dump** | A list of contact table in dump format, named by `chrs`, stored as an R object
|
|
|
| **contact_file_hic** | A hic file generated by Juicer tools. It should contain all chromosomes in `chrs`
|
|
|
-| **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). These compartments will be used as reference compartments for optimized bin_size selection. If `ref_genome = others`, an `annotation_track` should be provided (see below) and no optimized bin_size selection will be performed
|
|
|
-| **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:
|
|
|
+| **ref_genome** | One of 'hg19', 'hg38', 'mm9', 'mm10', 'others' (default). High quality compartment calls were generated for 'hg19' (hic data from GSE63525), 'hg38' (hic data from https://data.4dnucleome.org/files-processed/4DNFI1UEG1HD/), 'mm9' (hic data from GSM3959427), 'mm10' (hic data from http://hicfiles.s3.amazonaws.com/external/bonev/CN_mapq30.hic). These compartments will be used as reference compartments for optimized bin_size selection. If `ref_genome = others`, an `annotation_track` should be provided (see below) and no optimized bin_size selection will be performed
|
|
|
+| **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 when `ref_genome` is not in 'hg19', 'hg38', 'mm9', 'mm10' 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 reverse H3k9me3 signals)
|
|
|
| **contact_file_hic** | Path to the hic xx
|
|
|
| **bin_size** | numeric, the size of a bin in consistent with the contact table
|
|
|
| **save_dir** | the directory to save outputs
|
Yuanlong LIU