ReplaceAboveCutOff: Replace the Cq and amplification efficiency above cut off by...

In NPhogat/RTqPCR: A work flow for analysis and normalization of pre-processing RT-qPCR data

Description

Replace the Cq and amplification efficiency above cut off by non detects (NA) in object of class "RTqPCRBatch".

Usage

## S4 method for signature 'RTqPCRBatch'
ReplaceAboveCutOff(RTqPCRBatch, NewVal = NA,
  Cqcutoff = 38, effscutoff = 2, ...)

Arguments

NewVal	The new value (NA) to replace the values above cut off.
Cqcutoff	The minimum threshold Cq value above which the values will be replaced by NA.
effscutoff	The minimum efficiency above which the values will be replaced by NA.
...	Other parameters to be passed to downstream methods.
Object	of class RTqPCRBatch. It can be output of CqValues or ReplaceValue or ReplaceNAs or NonDetects.

Details

This function ReplaceAboveCutOff is specifically designed to replace Cq values and amplification efficiencies, which are above the cutoffs by NA. There will be no effect on remaining data. The best point to implement the ReplaceAboveCutOff function is when some values of Cq and amplification efficiencies are coming too large for their consideration, due to some manual, computational or instrumental error. So, the user can define the cutoffs for Cq values and amplification efficiencies appropriately, based on their experience. For further details, see also vignettes in RTqPCR package.

Value

"RTqPCRBatch" object with new exprs and effs slots.

Author(s)

Navneet Phogat, Matthias Kohl, [e-mail]

Examples

## Read in the raw fluorescent data

LC480.example <- file.path(path, "LC480_Example.txt") 
cycData.LC480 <- read.RTqPCR(LC480.example, PCRtype = "LC480")

## Read in the sample information data

SampleInfoLC480 <- file.path(path, "LC480_example_SampleInfo.txt")
samInfoLC480 <- read.RTqPCRSampleInfo(SampleInfoLC480, PCRtype = "LC480")

## Merge the fluorescence and sample information data through merge function

merge.LC480<-merge(cycData.LC480,samInfo.LC480) 

## Compute the Cq values and amplification efficiencies

Cqeffs.LC480 <- CqValues(merge.LC480, PCRtype = "LC480", Effmethod = "sigfit", baseline = "none")
Cqeffs.LC480 #To see the overview of data
exprs(Cqeffs.LC480)[1:5]  ##to visualise the first five CqValues
effs(Cqeffs.LC480)[1:5]  ##to visualise the first five amplification efficiencies
exprs(Cqeffs.LC480)  ##to visualise all Cq values
effs(Cqeffs.LC480)   ##to visualise all amplification efficiencies

## Replace the Cq values and amplification efficiencies above the user defined cutoffs by NA

Cqeffs.cutoff <- ReplaceAboveCutOff(Cqeffs.LC480, NewVal = NA, Cqcutoff = 38, effscutoff = 1)
Cqeffs.cutoff ## To see the overview of data
exprs(Cqeffs.cutoff)[1:5]  ## to visualise the first five Cq values 
effs(Cqeffs.cutoff)[1:5]  ## to visualise the first five amplification efficiencies
exprs(Cqeffs.cutoff)  ## to visualise all Cq values
effs(Cqeffs.cutoff)   ## to visualise all amplification efficiencies

## This function ReplaceAboveCutOff can also be implemented on the outputs of other functions ReplaceValue, 
## ReplaceNAs and NonDetects as well as on the output of itself (ReplaceAboveCutOff), if the user
## wants to define a new value of cutoffs smaller than previous one. For further details, see the vignettes
## of RTqPCR package.

NPhogat/RTqPCR documentation built on July 12, 2020, 12:56 p.m.