TimeCompare: Time-varying TAD boundary analysis

Description Usage Arguments Details Value Examples

View source: R/TimeCompare.R

Description

Time-varying TAD boundary analysis

Usage

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TimeCompare(
  cont_mats,
  resolution,
  z_thresh = 2,
  window_size = 15,
  gap_thresh = 0.2,
  groupings = NULL
)

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 n 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 more stringent detection of 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

groupings

Variable for defining groups of replicates at a given time point. Each group will be combined using consensus boundary scores. It should be a vector of equal length to cont_mats where each entry is a label corresponding to the group membership of the corresponding matrix. Default is NULL, implying one matrix per time point.

Details

Given a list of sparse 3 column, n x n, or n x (n+3) contact matrices representing different time points, TimeCompare identifies all TAD boundaries. Each TAD boundary is classified into six categories (Common, Dynamic, Early/Late Appearing and Early/Late Disappearing), based on how it changes over time.

Value

A list containing consensus TAD boundaries and overall scores

Examples

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# Read in data
data("time_mats")
# Find time varying TAD boundaries
diff_list <- TimeCompare(time_mats, resolution = 50000)

cresswellkg/TADCompare documentation built on Dec. 1, 2020, 10:35 p.m.