designOptim: Optimize N and R

Description Usage Arguments Value

Description

Optimize N and R

Usage

1
2
3
4
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 May 29, 2019, 3:42 a.m.