binarizeMFIbySD: Retrieve binary indicator of peptide signal presence based on...

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

Usage

binarizeMFIbySD(bbea.object,buffer.name="Buffer",plateVar="PlateNum",
         UR=c('PTID','Visit'),nSD=3,logMFI=TRUE,offset=0.5)

Arguments

bbea.object	bbea data object
buffer.name	buffer to use for reference signal
plateVar	column indicating batch/plate
UR	unit of replication
nSD	number of standard deviations to use as the cutoff before indicating a positive signal presence
logMFI	boolean for taking the log transform of the mean fluorescence intensity

Value

expressionSet

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),]
binary.db <- binarizeMFIbySD(bbea.object = bbeaEgg,
                             buffer.name = "Buffer",
                             plateVar = "Plate",
                             UR = 'PTID', 
                             nSD = 3) 
sampleNames(binary.db) <- sapply(strsplit(sampleNames(binary.db), "_"),tail, 1)
# can remove background (Buffer) wells
binary.db <- binary.db[, !grepl("Buffer", sampleNames(binary.db))]

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