# 1 Introduction

TADCompare is an R package for differential analysis of TAD boundaries. It is designed to work on a wide range of formats and resolutions of Hi-C data. TADCompare package contains four functions: TADCompare, TimeCompare, ConsensusTADs, and DiffPlot. TADCompare function allows for the identification of differential TAD boundaries between two contact matrices. TimeCompare function takes a set of contact matrices, one matrix per time point, identifies TAD boundaries, and classifies how they change over time. ConsensusTADs function takes a list of TADs and identifies a consensus of TAD boundaries across all matrices using our novel consensus boundary score. DiffPlot allows for visualization of TAD boundary differences between two matrices. The required input includes matrices in sparse 3-column format, $$n \times n$$, or $$n \times (n+3)$$ formats. This vignette provides a complete overview of input data formats.

# 2 Getting Started

## 2.1 Installation

BiocManager::install("TADCompare")
library(dplyr)
##
## Attaching package: 'dplyr'
## The following objects are masked from 'package:stats':
##
##     filter, lag
## The following objects are masked from 'package:base':
##
##     intersect, setdiff, setequal, union
library(SpectralTAD)
library(TADCompare)

# 3 Working with different types of data

## 3.1 Working with $$n \times n$$ matrices

$$n \times n$$ contact matrices are most commonly associated with data coming from the Bing Ren lab (http://chromosome.sdsc.edu/mouse/hi-c/download.html). These contact matrices are square and symmetric with entry $$ij$$ corresponding to the number of contacts between region $$i$$ and region $$j$$. Below is an example of a $$5 \times 5$$ region of an $$n \times n$$ contact matrix derived from Rao et al. 2014 data, GM12878 cell line (Rao et al. 2014), chromosome 22, 50kb resolution. Note the symmetry around the diagonal - the typical shape of chromatin interaction matrix. The figure was created using the pheatmap package.