makeAllNAs {NormqPCR} | R Documentation |
Make all Cq values for a given detector NA when the number of NAs for that detector is above a given threshold
makeAllNAs(qPCRBatch, ...) ## S4 method for signature 'qPCRBatch' makeAllNAs(qPCRBatch, contrastM, sampleMaxM)
qPCRBatch |
Expression set containing qPCR data. |
... |
Extra arguments, detailed below |
contrastM |
Contrast Matrix like that used in |
sampleMaxM |
Sample Max Matrix. Columns represent the different sample types. There is one value per column, which represents the max number of NAs allowed for that sample type. |
Make all NAs when number of NAs above a given threshold
qPCRBatch
object with a new exprs slot, everything else equal
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.
# read in the data 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",] # values before # make contrastM a <- c(0,0,1,1,0,0,1,1) # one for each sample type, with 1 representing b <- c(1,1,0,0,1,1,0,0) # position of sample type in the samplenames vector contM <- cbind(a,b) colnames(contM) <- c("case","control") # then give the names of each sample type rownames(contM) <- sampleNames(qPCRBatch.taqman) # and the rows of the matrix contM # make sampleMaxM sMaxM <- t(as.matrix(c(3,3))) # now make the sample max matrix colnames(sMaxM) <- c("case","control") # make sure these line up with samples sMaxM # function qPCRBatch.taqman.replaced <- makeAllNAs(qPCRBatch.taqman, contM, sMaxM) exprs(qPCRBatch.taqman.replaced)["Ccl20.Rn00570287_m1",]