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Run RAS change-point detection and map peaks to base pairs

Source: R/ingest.R
call_peaks.Rd

Wraps RAS::ras_detect and RAS::ras_validate. Correctly maps the validated tau_hats (which are full-SNP-scale indices) back to base-pair positions.

Usage

call_peaks(
  scan,
  bp_per_snp,
  window_size = 20,
  slope_check_window_size = 8,
  slope_threshold = 1e-04,
  davies_threshold = 1e-05,
  min_signal = 2.5,
  skip = 10
)

Arguments

scan

Output of scan_ss.

bp_per_snp

Base-pair positions aligned to the SNPs given to scan_ss.

window_size

CPD window size.

slope_check_window_size

CPD slope check window.

slope_threshold

CPD slope p-value threshold.

davies_threshold

CPD Davies p-value threshold.

min_signal

Minimum RAS height to validate a peak.

skip

The skip1 parameter used in scan_ss.

Value

List with snp_index, grid_index, and bp.