weight_phases: Weighting phases

In CL-CHEN-Lab/RepliSeq: Repliseq

Description

Using a simulation of the S-phase (active forks in function of the percentage replicated genome), this function calculates a normalization factor for each phase based on the FACS gates and G1/G2 peaks

Usage

weight_phases(
  rs_assay,
  G1_peak,
  G2_peak,
  gates,
  SimSPhase = NA,
  TotalReads = NA
)

Arguments

rs_assay	a Repli-seq assay (data.frame) loaded with readRS() and formatted as chr,start,stop,S1,...,Sx
G1_peak	aproximate position of the G1 peak
G2_peak	aproximate position of the G2 peak
gates	a data.frame containing start and end of each gate ordered as in rs_assay
SimSPhase	a user constumise simulation of the S-phase progression (data.frame) formatted as Percentage of replicated DNA, Number of active forks
TotalReads	Totala ammount of reads for normalization, by defaul 15000000 per phase

Value

A named vector containing the normalization factors for each phase to use with normalizeRS

CL-CHEN-Lab/RepliSeq documentation built on Sept. 11, 2021, 12:04 p.m.