makeAllNewVal: Make all Cq values NA

In jimrperkins/NormqPCR: Functions for normalisation of RT-qPCR data

Description

Make all Cq values for a given detector NA when the number of NAs for that detector is above a given threshold

Usage

makeAllNewVal(qPCRBatch, ...)

## S4 method for signature 'qPCRBatch'
makeAllNewVal(qPCRBatch, contrastM, sampleMaxM, newVal)

Arguments

qPCRBatch	Expression set containing qPCR data.
...	Extra arguments, detailed below
contrastM	Contrast Matrix like that used in limma. Columns represent the different samples types, rows are the different samples, with a 1 or 0 in the matrix indicating which sample types the different samples belong to.
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.
newVal	New value to give the values in the group where the NAs are above the threshold.

Details

Make all a given value when number of NAs above a given threshold, with different thresholds for the different sample classes, using sMaxM and contM to provide this information, as detailed below.

Value

qPCRBatch object with a new exprs slot, everything else equal

Author(s)

James Perkins [e-mail]

References

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.

Examples

  # 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 <- makeAllNewVal(qPCRBatch.taqman, contM, sMaxM)
  exprs(qPCRBatch.taqman.replaced)["Ccl20.Rn00570287_m1",]

jimrperkins/NormqPCR documentation built on March 6, 2020, 1:06 a.m.