Description Usage Arguments Value Examples
Calculates p-values under the negative binomial model. Subsequently regroups putative interactions by bait, rather than by distance, to prepare them for parallel RJMCMC processing. Generates a separate file for each bait. Paths are stored in baitlist.txt, which serves as a to-do list for peaky().
1 | split_baits_fs(bins_dir, residuals_dir, indices, output_dir, plots = TRUE)
|
bins_dir |
Directory containing putative interactions that are binned by distance. |
residuals_dir |
Directory where the adjusted read counts from each distance bin are stored. |
indices |
Indices of distance bins whose baits are processed. These must all have had null models fitted. |
output_dir |
Directory where all putative interactive will be stored, one file per bait. Will be created if it does not exist. |
plots |
Whether adjusted readcounts are to be plotted aganst distance and stored for each bait. |
The output directory.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 | base = system.file("extdata",package="peaky")
interactions_file = paste0(base,"/counts.tsv")
bins_dir = paste0(base,"/bins")
fragments_file = paste0(base,"/fragments.bed")
bin_interactions_fs(interactions_file, fragments_file, output_dir=bins_dir)
fits_dir = paste0(base,"/fits")
for(bin_index in 1:5){
## Not run: model_bin_fs(bins_dir,bin_index,output_dir=fits_dir,subsample_size=1000)
}
baits_dir = paste0(base,"/baits")
## Not run: split_baits_fs(bins_dir,residuals_dir = fits_dir, indices=1:5, output_dir = baits_dir)
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