Hawkes Genomics

R package to Estimate parameters for a hawkes model over spatial positions using this c++ implementation.

Requirement

A C++ compiler supporting C++14 is required:

g++ >= 5.0
clang++ >= 3.4
for any other compiler, check that it supports the -std=c++14 flag

R >= 4.3 (the package may works on older version of R)

Installation

You need the package remotes to install hawkesGenomics from this repository

install.packages("remotes")

Then you can install hawkesGenomics with this command

remotes::install_git("https://github.com/franckpicard/hawkes_genomics", force = T)

Example

We are going to analyse a subset of the replication origin on the chromosme 1 of hg19.

library("hawkesGenomics")

preprocess data

beds <- preprocess_bed(
  files = c(
    system.file("extdata", "oris.bed.gz", package = "hawkesGenomics"),
    system.file("extdata", "CGI.bed.gz", package = "hawkesGenomics"),
    system.file("extdata", "G4plus.bed.gz", package = "hawkesGenomics")
  ),
  names = c("Oris", "CGI", "G4plus")
)

hawkes computation

res <- compute_hawkes_histogram(
  files = beds$preprocess_beds,
  names = beds$names,
  K = 5,
  delta = 1e4
)

plot data

plot_histogram(res, K = 5, delta = 1e4)