README.md

In hillarykoch/locdiffr: analysis of LOCal DIFFerences in chromatin aRchitecture

locdiffr (Analysis of LOCal DIFFerences in chromatin aRchitecture)

Dependencies

1. This package was developed in R version 3.6.2, back compatability is not guaranteed

2. To use this package, you need a compiler that has support for C++11, such as

   • GCC: see here, for example
   • clang: see here

Installation

Installation is easy with the R package devtools. If you don't already have devtools installed, you will first need to type (from within R)

install.packages("devtools")

With devtools installed, simply enter the following:

devtools::install_github("hillarykoch/locdiffr", build_vignettes = TRUE)

Installation may take a couple of minutes due to building the vignette. The vignette contains all of the necessary instructions to run locdiffr. To view the vignette, enter the following within R:

browseVignettes(package = "locdiffr")

Input format

To begin the analysis, you need file paths to all of the data, split into two groups. The data should be in the following tab-delimited format:

| Loc1 | Loc2 | Counts | |------|--------|--------| | 0 | 0 | 100 | | 0 | 50000 | 88 | | 0 | 100000 | 40 |

Here, Loc1 is the start of the first bin, Loc2 the start of the second bin, and counts indicating the read counts for the interactions between those 2 bins. The value in Loc1 should always be less than or equal to the value in Loc2. An individual dataset is intended to be Hi-C data from an entire chromosome. Chromosomes should be analyzed separately.

hillarykoch/locdiffr documentation built on April 25, 2021, 6:26 p.m.