replaceAboveCutOff: Replace Cq values with new value

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

Description

Replace Cq values above a given threshold with a new value

Usage

replaceAboveCutOff(qPCRBatch, ...)

## S4 method for signature 'qPCRBatch'
replaceAboveCutOff(qPCRBatch, newVal=NA, cutOff=38)

Arguments

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

Details

Replaces values in the exprs slot of the qPCRBatch object that are above a threshold value with a new number

Value

qPCRBatch object with a new exprs slot

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

  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",]

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