replaceAboveCutOff {NormqPCR} | R Documentation |
Replace Cq values above a given threshold with a new value
replaceAboveCutOff(qPCRBatch, ...) ## S4 method for signature 'qPCRBatch' replaceAboveCutOff(qPCRBatch, newVal=NA, cutOff=38)
qPCRBatch |
Expression set containing qPCR data. |
... |
Extra arguments, detailed below |
newVal |
The new value with which to replace the values above the cutoff |
cutOff |
the minimal threshold above which the values will be replaced |
Replaces values in the exprs slot of the qPCRBatch
object that are above a threshold value with a new number
qPCRBatch
object with a new exprs slot
James Perkins jimrperkins@gmail.com
Perkins, JR, Dawes, JM, McMahon, SB, Bennett, DL, Orengo, C, Kohl, M (2012). ReadqPCR and NormqPCR: R packages for the reading, quality checking and normalisation of RT-qPCR quantification cycle (Cq) data. BMC Genomics, 13, 1:296.
path <- system.file("exData", package = "NormqPCR") taqman.example <- file.path(path, "example.txt") qPCRBatch.taqman <- read.taqman(taqman.example) exprs(qPCRBatch.taqman)["Ccl20.Rn00570287_m1",] qPCRBatch.taqman.replaced <- replaceAboveCutOff(qPCRBatch.taqman, newVal = NA, cutOff = 35) exprs(qPCRBatch.taqman.replaced)["Ccl20.Rn00570287_m1",]