|
|
@@ -114,11 +114,11 @@ CALDER_sub_domains(intermediate_data_file,
|
|
|
| Parameters | Description
|
|
|
| --------------------- | ----------------------- |
|
|
|
| **contact_tab_straw** |
|
|
|
-| **ref_genome** | One of 'hg19', 'hg38', 'mm9', 'mm10', or 'others' by default.
|
|
|
+| **ref_genome** | One of 'hg19', 'hg38', 'mm9', 'mm10', 'others' (default).
|
|
|
| **annotation_track** | A table in data.frame or data.table format
|
|
|
| **contact_file_hic** | Path to the hic
|
|
|
-| **subcomp** | Optional: Assigning sub-compartments based on PC magnitude values using HMM segmentation
|
|
|
-| **fithic** | Run [Fit-Hi-C](https://github.com/ay-lab/fithic) to identify loops before running dloop (Optional but recommended)
|
|
|
+| **chrs** | vector of character or numeric. Chromosome names to be analyzed.
|
|
|
+| **bin_size** | numeric, the size of a bin in consistent with the contact table
|
|
|
| **dloop** | Find differential loops anchored in at least one of the differential compartments across the samples (Optional but recommended)
|
|
|
| **viz** | Generate IGV vizualization HTML file. Must have performed other steps in order (optional ones not strictly necessary) before this one.
|
|
|
| **enrich** | Perform gene enrichment analysis (GSEA) of genes in differential compartments/loops
|
Yuanlong LIU