ConsensusTADs {TADCompare} | R Documentation

## Consensus boundary identification

### Description

Consensus boundary identification

### Usage

    ConsensusTADs(
      cont_mats,
      resolution,
      z_thresh = 3,
      window_size = 15,
      gap_thresh = 0.2
    )

### Arguments

`cont_mats` | List of contact matrices in either sparse 3 column, n x n or n x (n+3) form where the first three columns are coordinates in BED format. See "Input_Data" vignette for more information. If an x n matrix is used, the column names must correspond to the start point of the corresponding bin. Required.
`resolution` | Resolution of the data. Used to assign TAD boundaries to genomic regions. If not provided, resolution will be estimated from column names of the first matrix. Default is "auto"
`z_thresh` | Threshold for boundary score. Higher values result in a higher threshold for differential TADs. Default is 3.
`window_size` | Size of sliding window for TAD detection, measured in bins. Results should be consistent Default is 15.
`gap_thresh` | Required % of non-zero entries before a region will be considered non-informative and excluded. Default is .2

### Details

Given a list of sparse 3 column, n x n , or n x (n+3) contact matrices, ConsensusTADs provides the set of consensus TAD boundaries across them. Consensus TADs are defined by the consensus boundary score, a score measuring TAD boundary likelihood across all matrices.

### Value

A list containing consensus TAD boundaries and overall scores

- Consensus - Data frame containing location of all consensus boundaries. Coordinate is the region of the genome, Sample columns correspond to individual boundary scores. Consensus_Score is consensus boundary score.

- All_Regions - Data frame containing consensus scores for all regions. All columns are identiical to the Consensus object.

### Examples

    # Read in data
    data("time_mats")
    # Find consensus TAD boundaries
    diff_list <- ConsensusTADs(time_mats, resolution = 50000)

[Package TADCompare version 1.2.0 Index]