NOMIS normalized adjusted object — bc

This function returns a pmart object that has been undergone NOMIS normalization regarding batch effect correction

Usage

bc_nomis(omicsData, is_cname, is_val, num_pc = 2)

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.
is_cname: character string giving the name of the column in omicsData$e_meta that contains the factor variable indicating whether the molecule is internal standards or not
is_val: value giving the name/value in the is_cname column that indicates that the sample is an Internal Standards sample
num_pc: numeric variable providing the number of principal components for NOMIS to consider when running the batch correction method, defaults to 2

Value

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

Author

Damon Leach

Examples

library(malbacR)
library(pmartR)
data("pmart_mix")
pmart_mix <- group_designation(pmart_mix,main_effects = "BatchNum",batch_id = "BatchNum")
mix_nomis_abundance <- bc_nomis(omicsData = pmart_mix, is_cname = "tag", is_val = "IS", num_pc = 2)
#> Joining with `by = join_by(Metabolite)`