gi_list_topdom {HiCDCPlus} | R Documentation

## gi_list_topdom

### Description

This function converts a gi_list instance with ICE normalized counts into TAD annotations through an implementation of TopDom v0.0.2 (https://github.com/HenrikBengtsson/TopDom) adapted as `TopDom` at this package. If you're using this function, please cite TopDom according to the documentation at https://github.com/HenrikBengtsson/TopDom/blob/0.0.2/docs/

### Usage

    gi_list_topdom(
      gi_list,
      chrs = NULL,
      file_out = FALSE,
      fpath = NULL,
      window.size = 5,
      verbose = FALSE
    )

### Arguments

`gi_list` | List of `GenomicInteractions` objects where each object named with chromosomes contains intrachromosomal interaction information (see `?gi_list_validate` for a detailed explanation of valid `gi_list` instances).
`chrs` | select a subset of chromosomes' e.g., c('chr21','chr22'). Defaults to chromosomes in `gi_list`.
`file_out` | If true, outputs TAD annotations into files with paths beginning with `fpath`. Defaults to FALSE
`fpath` | Outputs TAD annotations into files with paths beginning in `fpath`.
`window.size` | integer, number of bins to extend. Defaults to 5.
`verbose` | TRUE if you would like to troubleshoot TopDom.

### Value

a list instance with TAD annotation reporting for each chromosome

### Examples

    hic_path<-system.file("extdata", "GSE63525_HMEC_combined_example.hic",
    package = "HiCDCPlus")
    gi_list<-hic2icenorm_gi_list(hic_path,binsize=50e3,chrs='chr22')
    tads<-gi_list_topdom(gi_list)

[Package HiCDCPlus version 1.0.0 Index]