omixerSpecific: Sample List Regeneration

In molepi/Omixer: Omixer: multivariate and reproducible sample randomization to proactively counter batch effects in omics studies

Description

Regenerate an Omixer-produced randomized sample list quickly, after setting up the random environement from omixerRand

Usage

omixerSpecific(
  df,
  sampleId = "sampleId",
  block = "block",
  wells,
  div = "none",
  positional = FALSE,
  plateNum = 1,
  layout,
  mask = 0,
  techVars,
  randVars
)

Arguments

df	Sample list
sampleId	String specifying sample ID variable
block	Paired sample identifier
wells	Number of wells on a plate
div	Plate subdivisions
positional	Logical indicator of positional batch effects
plateNum	Number of plates
layout	Custom plate layout as data frame
mask	Wells to be left empty
techVars	Technical covariates
randVars	Randomization variables

Value

Chosen layout as a data frame

Examples

library(tibble)
library(forcats)
library(stringr)

sampleList <- tibble(sampleId=str_pad(1:48, 4, pad="0"),
sex=as_factor(sample(c("m", "f"), 48, replace=TRUE)), 
age=round(rnorm(48, mean=30, sd=8), 0), 
smoke=as_factor(sample(c("yes", "ex", "never"), 48, replace=TRUE)),
date=sample(seq(as.Date('2008/01/01'), as.Date('2016/01/01'), 
               by="day"), 48))
               
randVars <- c("sex", "age", "smoke", "date")

omixerLayout <- omixerSpecific(sampleList, sampleId="sampleId", 
block="block", wells=48, div="row", 
plateNum=1, randVars=randVars)

molepi/Omixer documentation built on Jan. 28, 2021, 4:56 p.m.