ReplaceNAs: Replace the all the non detects of Cq and amplification...

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

Description

Replace all the non detects of Cq and amplification efficiencies by user defined values in object of "RTqPCRBatch".

Usage

## S4 method for signature 'RTqPCRBatch'
ReplaceNAs(RTqPCRBatch, NewCqNA, NeweffsNA, ...)

Arguments

RTqPCRBatch	Object of class RTqPCRBatch. It can be output of CqValues or ReplaceValue or ReplaceAboveCutOff or NonDetects.
NewCqNA	New user defined value of Cq for replacing non - detects (NA) of Cq.
NeweffsNA	New user defined value of amplification efficiency for replacing non detects (NA) of amplification efficiency.
...	other parameters to be passed to downstream methods.

Details

ReplaceNAs works on the object of RTqPCRBatch, which is obtained through implementation of CqValues or ReplaceAboveCutOff or ReplaceValue or NonDetects. The three functions ReplaceNAs, NonDetects and ReplaceAboveCutOff can be called among themselves as well as for implementation on results of CqValues function. The functions for replacing the values are mainly designed to have a better control of user over the resultant data of Cq values and amplification efficiencies. For further details, see also vignettes.

Value

"RTqPCRBatch" object with new exprs and effs slots.

Author(s)

Navneet Phogat, Matthias Kohl, [e-mail]

Examples

## i) Read in the raw fluorescent data

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

## ii) Read in the sample information data

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

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

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

## iv) 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

## v) Replace the non-detects (NA) by user defined values

Cqeffs.ReNA <- ReplaceNAs(Cqeffs.LC480, NewCqNA = 35, NeweffsNA = 1)
Cqeffs.ReNA ## To see the overview of data
exprs(Cqeffs.ReNA)[1:5]  ## to visualise the first five Cq values 
effs(Cqeffs.ReNA)[1:5]  ## to visualise the first five amplification efficiencies
exprs(Cqeffs.ReNA)  ## to visualise all Cq values
effs(Cqeffs.ReNA)   ## to visualise all amplification efficiencies

## This function ReplaceNAs can also be implemented on the outputs of other functions ReplaceValue, 
## ReplaceAboveCutOff and NonDetects and for that the user doesn't need to calculate the CqValues 
## again and again. For detail, check the vignettes of RTqPCR package.  
   

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