ComputeNRQs: Compute Normalized Relative Quantities

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

Description

This function computes normalized relative quantities (NRQs) for a qPCRBatch.

Usage

ComputeNRQs(qPCRBatch, ...)
## S4 method for signature 'qPCRBatch'
ComputeNRQs(qPCRBatch, hkgs)

Arguments

qPCRBatch	an object of class qPCRBatch.
hkgs	Names of reference/housekeeping genes.
...	other parameters to be passed to downstream methods.

Details

Allows the user to normalized relative quantities as defined in Hellemanns et al. (2007).

Value

Object of class "qPCRBatch".

Author(s)

Nor Izayu Abdul Rahman, Matthias Kohl [e-mail]

References

Jan Hellemans, Geert Mortier, Anne De Paepe, Frank Speleman and Jo Vandesompele (2007). qBase relative quantification framework and software for management and automated analysis of real-time quantitative PCR data. Genome Biology, 8:R19

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.

See Also

qPCRBatch-class

Examples

  ## Example data
  path <- system.file("exData", package = "ReadqPCR")
  qPCR.example <- file.path(path, "qPCR.example.txt")
  Cq.data <- read.qPCR(qPCR.example)

  ## combine technichal replicates
  Cq.data1 <- combineTechRepsWithSD(Cq.data)

  ## add efficiencies
  Effs <- file.path(path, "Efficiencies.txt")
  Cq.effs <- read.table(file = Effs, row.names = 1, header = TRUE)
  rownames(Cq.effs) <- featureNames(Cq.data1)
  effs(Cq.data1) <- as.matrix(Cq.effs[,"efficiency",drop = FALSE])
  se.effs(Cq.data1) <- as.matrix(Cq.effs[,"SD.efficiency",drop = FALSE])
  
  ##
  res <- ComputeNRQs(Cq.data1, hkgs = c("gene_az", "gene_gx"))
  ## NRQs
  exprs(res)
  ## SD of NRQs
  se.exprs(res)

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