|
|
@@ -111,6 +111,19 @@ CALDER_sub_domains(intermediate_data_file,
|
|
|
* `save_intermediate_data`: logical. If TRUE, an intermediate_data will be saved. This file can be used for computing nested sub-domains later on
|
|
|
* `genome`: string. Specifies the genome assembly (Default="hg19").
|
|
|
|
|
|
+| --Parameters | Meaning
|
|
|
+| --------------------- | ----------------------- |
|
|
|
+| **cis** | Find compartments on a cis interaction matrix
|
|
|
+| **trans** | Find compartments on a trans interaction matrix
|
|
|
+| **select** | Selection of best PC for downstream analysis [Must be after cis or trans step]
|
|
|
+| **analyze** | Perform differential analysis on selected PC's [Must be after select step]
|
|
|
+| **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)
|
|
|
+| **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
|
|
|
+
|
|
|
+
|
|
|
### Output:
|
|
|
|
|
|
#### chrxx_domain_hierachy.tsv
|
Yuanlong LIU