ChAMP_QC_Pipeline_Frome_Beta_Value: ChAMP QC Pipeline for beta matrix

In ProfessionalFarmer/loonR: Common function in bioinformatics analysis

ChAMP QC Pipeline for beta matrix

Description

ChAMP QC Pipeline for beta matrix

Usage

ChAMP_QC_Pipeline_Frome_Beta_Value(
  Sample.beta.df = NULL,
  Sample.Group = "",
  Slide = "",
  arraytype = c("450K", "EPIC"),
  CpG.GUI = FALSE,
  QC.GUI = FALSE,
  combat = FALSE,
  batchname = c("Slide"),
  cores = 50
)

Arguments

Sample.beta.df	Column is sample
arraytype	450K or EPIC
CpG.GUI	If use CpG.GUI
combat	If perform combat to remove batch effect
batchname	Batch variable name. Default is c("Slide")
cores

Examples

library(ChAMP)
testDir=system.file("extdata",package="ChAMPdata")
myImport <- champ.import(testDir)

beta.df = myImport$beta
group = myImport$pd$Sample_Group

########### Step 1
res = loonR::ChAMP_QC_Pipeline_Frome_Beta_Value(Sample.beta.df=beta.df, Sample.Group=group)
myLoad = res$myLoad

########### Step 2
res = res$followAnalysisImputeQCNormCombat(arraytype="450K")
head(res$myNorm)

ProfessionalFarmer/loonR documentation built on Oct. 9, 2024, 9:56 p.m.