Get started

library(hawkesGenomics)

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")
)
beds
#> # A tibble: 3 × 5
#> # Groups:   files [3]
#>   files                             names interval_size beds     preprocess_beds
#>   <chr>                             <chr>         <dbl> <list>   <chr>          
#> 1 /home/runner/work/_temp/Library/… G4pl…          25.6 <tibble> /tmp/Rtmpl3saV…
#> 2 /home/runner/work/_temp/Library/… CGI           766.  <tibble> /tmp/Rtmpl3saV…
#> 3 /home/runner/work/_temp/Library/… Oris          883.  <tibble> /tmp/Rtmpl3saV…

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)

plot_convolution(res, width = beds$interval_size, K = 5, delta = 1e4)