getAveragesByReps: From an expressionset, calculate replicate averages

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

Usage

getAveragesByReps(eset, UR=c("PTID", "Plate"))

Arguments

eset	expressionSet of peptide expression
UR	unit of replication (e.g., patient, visit)

Author(s)

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

Examples

data(Egg)
# adding patient data
bbeaEgg$pData <- mutate(bbeaEgg$pData, 
                     PTID = sapply(strsplit(Sample, "-",fixed=TRUE), head, 1),
                     SampleType = ifelse(grepl("Buff", Sample),"Buffer",
                                         ifelse(grepl("PP|NP", Sample),
                                                sapply(strsplit(Sample, "-",fixed=TRUE),head, 1), "Patient")))
PDm <- merge(bbeaEgg$pData, PDegg, by = "PTID", all.x = TRUE)
rownames(PDm) <- PDm$File
bbeaEgg$pData <- PDm[colnames(bbeaEgg$Median),]

# convert MFI to normlaized MFI
bbeaN <- MFI2nMFI(bbeaEgg, offset = 0.5, rmNeg = TRUE)

# chnage to the ExpressionSet object
eset <- nMFI2Eset(nMFI.object = bbeaN)

# Average technical replicates
eset.avg <- getAveragesByReps(eset, UR = 'PTID')

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