peaky_fs: Wrapper for peaky() that interacts with the filesystem
In cqgd/pky: Capture Hi-C calling algorithm

Description Usage Arguments Value Details

Fits additive models of peaks of varying strengths in various locations to the adjusted readcounts via RJMCMC, and stores these models on disk.

peaky_fs(
  baitlist,
  index,
  output_dir,
  omega_power,
  iterations = 1e+06,
  min_interactions = 20
)

`baitlist`	Path to the list of baits to be processed.
`index`	Which bait on the list to process, with 1 corresponding to the first one on the list.
`output_dir`	Directory where all RJMCMC results will be stored. Will be created if it does not exist.
`omega_power`	Expected decay of adjusted read counts around a truly interacting prey. See details.
`iterations`	Number of models to parametrize. Greated numbers should lead to increased reproducibility.
`min_interactions`	Minimum requirement for the number of prey fragments (and thus counts) associated with a bait, baits with fewer are skipped.

List containing the model output directory and the models themselves.

The steepness of the function to be fitted to putative peaks is determined by ω according to β exp(-|ω * d|), where β represents peak height and d the distance from the center of the peak in bp.

cqgd/pky documentation built on Dec. 13, 2020, 3:32 a.m.