omixerSheet: Sample Sheet Generation

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

Description

This function will generate visually intuitive plate layouts for the wet lab, with the option to colour code different types of samples (e.g. for studies investigating multiple tissues).

Usage

omixerSheet(omixerLayout = omixerLayout, group)

Arguments

omixerLayout	Randomized sample list
group	Colour-coding indicator

Value

PDF of sample layout in working directory

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 <- omixerRand(sampleList, sampleId="sampleId", 
block="block", iterNum=10, wells=48, div="row", 
plateNum=1, randVars=randVars)

omixerSheet(omixerLayout)

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