Description Usage Arguments Value Examples
Places putative interactions into equally-sized bins based on the distances they span.
1 2 3 4 5 6 7 8 | bin_interactions(
interactions,
fragments,
bins = 5,
min_dist = 2500,
max_dist = Inf,
log_file = NA
)
|
interactions |
Data table containing putative interactions. Columns called baitID, preyID, N, storing the bait fragment ID, prey fragment ID and readcount, respectively. |
fragments |
Data table containing fragment information. Columns called chrom, chromStart, chromEnd, ID, storing the chromosome, starting coordinate, ending coordinate and ID of a fragment, respectively. |
bins |
Number of bins to place the interactions into. |
min_dist |
Minimum distance interactions must span to be included in the analysis. Distance is defined between fragment midpoints. |
max_dist |
Maximum distance interactions can span to be included in the analysis. Distance is defined between fragment midpoints. |
log_file |
Path to a log file. |
List containing the binned interactions ($interactions) and an overview of bins ($bins).
1 2 3 4 5 6 7 8 9 10 | base = system.file("extdata",package="peaky")
interactions_file = paste0(base,"/counts.tsv")
fragments_file = paste0(base,"/fragments.bed")
interactions = data.table::fread(interactions_file)
fragments = data.table::fread(fragments_file)
## Not run: BI = bin_interactions(interactions, fragments, bins=5)
print(BI)
|
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