pvcaBatchAssess.bbea: Principal Variance Component Analysis of samples from...

In msuprun/bbeaR: an R package and framework for epitope-specific antibody profiling

Usage

pvcaBatchAssess.bbea(eset, batch.factors, threshold, include.inter=NULL)

Arguments

eset	expressionSet of peptide data
batch.factors	batch metadata
threshold	pre-defined threshold for principal components containing an amount of variation
include.inter	interactions to include

Author(s)

Maria Suprun, Randall J. Ellis, Mayte Suárez-Fariñas

Examples

data(Milk)
bbeaN <- MFI2nMFI(bbea, offset = 0.5, rmNeg = TRUE) 
eset <- nMFI2Eset(nMFI.object = bbeaN)
pvca.obj<-pvcaBatchAssess.bbea(eset,
                               threshold=0.8,
                               batch.factors=c('Plate','Treatment','Visit',"SUBJECT.ID"),  
                               include.inter='Treatment:Visit') 
pvca.plot(pvca.obj, fname='PVCA.Plate.Covariates', ht=4, wd=5.5,
          order=c('Plate','Treatment','Visit','Treatment x Visit',"SUBJECT.ID",'resid'))

msuprun/bbeaR documentation built on Jan. 31, 2021, 6:49 p.m.