designOptim: Optimize N and R

In liupeng2117/MethylSeqDesign: MethylSeqDesign: a power calucation and study design tool for Methyl-Seq

Optimize N and R

Description

Optimize N and R

Usage

designOptim(EDR.result, pilot.R, R = c(1/10, 1/8, 1/6, 1/4, 1/2, 1, 1.5,
  2), N = seq(4, 50, 2), targetEDR = NULL, budget = NULL,
  price_per_lane = 1500, fix_price_per_sample = 300,
  depth_per_lane = 250)

Arguments

EDR.result	a MethylSeqDesign object
pilot.R	the sequencing depth of pilot data in number of lanes
R	the targeted sequencing depth in number of lanes, input can be a vector.
N	the targeted sample size per group, input can be a vector.
targetEDR	the target EDR to achieve
budget	the budget limit
price_per_lane	the price per lane for Methyl-Seq
fix_price_per_sample	the fixed part of the price per sample including the bisulfite treatment
depth_per_lane	the total number of reads per lane in millions

Value

a list of three elements. The first element gives the best N and R combination, and optimal EDR/cost given budget/target EDR. The second element is a plot of admissible/inadmissible N and R combinations. The third element is a plot of cost and EDR.

liupeng2117/MethylSeqDesign documentation built on June 28, 2023, 7:09 a.m.