ocampo2: Get ocampo parameters per instance (Tamas version using ccv)

In musikutiv/tsTools: Toolbox for Functional Genomics Data Processing in R

Get ocampo parameters per instance (Tamas version using ccv)

Description

Get ocampo parameters per instance (Tamas version using ccv)

Usage

ocampo2(coverage = coverage, references = reference, beforeRef = 200,
  afterRef = 1000, smoothingWindow = 100, spacing.low = 130,
  spacing.high = 220, shift.low = -70, shift.high = 70, mc.cores = 2,
  sigma_scaled = FALSE)

Arguments

coverage	a coverage object (RleList as returned by coverage)
references	reference regions data frame with columns (chr, start, end, strand). rownames will serve as id for output table
beforeRef	bps before reference to take for shift estimation
afterRef	bps after reference to take for shift estimation
smoothingWindow	size of the smoothing window.
spacing.low	minimum spacing allowed
spacing.high	maximum spacing allowed
shift.low	minimum shift allowed
shift.high	maximum shift allowed
sigma_scaled	scaling sigma for array model (recommended). Default FALSE
spacing.high	maximum spacing allowed

Value

a data frame with columns r (correlation), space, and shift for each reference provided

musikutiv/tsTools documentation built on June 6, 2023, 1:39 a.m.