EigenMS adjusted object — bc

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

Usage

bc_eigenMS(omicsData)

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.

Value

Object of same class as omicsData that has been undergone EigenMS 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")
amide_eigen <- bc_eigenMS(omicsData = pmart_amide)
#> Data dimentions: 500642
#> Treatment groups: 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
#> Selecting complete peptides
#> Got 2+ treatment grps
#> The following object is masked from TREATS (pos = 7):
#> 
#>     TREATS
#> The following object is masked from TREATS (pos = 8):
#> 
#>     TREATS
#> Computing SVD, estimating Eigentrends...
#> Number of treatments: 3
#> Number of complete peptides (and samples) used in SVD
#> 372642
#> Number of treatment groups (in svd.id): 3
#> Starting Bootstrap.....
#> Iteration 50
#> Iteration 100
#> Iteration 150
#> Iteration 200
#> Iteration 250
#> Iteration 300
#> Iteration 350
#> Iteration 400
#> Iteration 450
#> Iteration 500
#> Number of bias trends automatically detected 8
#> Preparing to plot...
#> Unique number of treatment combinations:3
#> Normalizing...
#> Processing peptide 100
#> Processing peptide 200
#> Processing peptide 300
#> Processing peptide 400
#> Processing peptide 500
#> Done with normalization!!!