SERRF batch correction — bc

This function returns a pmart object that has been undergone SERRF batch effect correction

Usage

bc_serrf(omicsData, sampletype_cname, test_val, group_cname)

Arguments

omicsData: an object of the class 'pepData', 'proData', 'metabData', 'lipidData', or 'nmrData', usually created by as.pepData, as.proData, as.metabData, as.lipidData, or as.nmrData, respectively.
sampletype_cname: character string giving the name of the column in omicsData$f_data that contains the sample type information (such as quality control samples)
test_val: character string giving the name of the value within the column sampletype_cname to be used as the testing value for SERRF
group_cname: character string giving the name of the column in omicsData$f_data that contians the group information

Value

Object of same class as omicsData that has been undergone SERRF normalization

Author

Damon Leach

Examples

library(malbacR)
library(pmartR)
data("pmart_amide")
pmart_amide <- edata_transform(pmart_amide,"log2")
pmart_amide <- group_designation(pmart_amide,main_effects = "group",batch_id = "batch")
impObj <- imputation(omicsData = pmart_amide)
amide_imp <- apply_imputation(imputeData = impObj, omicsData = pmart_amide)
amide_imp_abund <- edata_transform(amide_imp,"abundance")
amide_serrf_abundance <- bc_serrf(omicsData = amide_imp_abund,sampletype_cname = "group",test_val = "QC",group_cname = "group")
#> Joining with `by = join_by(batch)`