ReplaceValue: Replace the specific Cq value and amplification efficiency by...

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

Description

Replace the specific Cq and amplification efficiency value by user defined values or NA for Cq and amplification efficiencies in the object of class "RTqPCRBatch".

Usage

## S4 method for signature 'RTqPCRBatch'
ReplaceValue(RTqPCRBatch, NewCq = 38, Neweffs = 2,
  Cqrow = 30, effsrow = 30, ...)

Arguments

RTqPCRBatch	Object of class RTqPCRBatch. It can be output of CqValues or ReplaceValue or ReplaceNAs or NonDetects or ReplaceAboveCutOff.
NewCq	New User defined value of Cq to replace a specific Cq value. It can be defined as NA too.
Neweffs	New user defined value of amplification efficiency to replace a specific amplification efficiency. It can be defined as NA too.
Cqrow	The specific row of Cq in exprs of object RTqPCRBatch where the new value of Cq is to be placed.
effsrow	The specific row of amplification efficiency in effs of object RTqPCRBatch where the new value of amplification efficiency is to be placed.
...	Other parameters to be passed to downstream methods.

Details

The user can implement the ReplaceValue function if user wants to change any specific Cq value or amplification efficiency by another value or NA, without changing the other data. For further details, see the vignettes in RTqPCR package.

Value

"RTqPCRBatch" object with a 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 specific Cq value and amplification efficiency by user defined values

Cqeffs.value <- ReplaceValue(Cqeffs.LC480, NewCq = 35, Neweffs = 1, Cqrow = 30, effsrow = 30)
Cqeffs.value ## To see the overview of data
exprs(Cqeffs.value)[1:5]  ## to visualise the first five Cq values 
effs(Cqeffs.value)[1:5]  ## to visualise the first five amplification efficiencies
exprs(Cqeffs.value)  ## to visualise all Cq values
effs(Cqeffs.value)   ## to visualise all amplification efficiencies

## This function ReplaceValue can also be implemented on the output of other functions ReplaceNAs, 
## ReplaceAboveCutOff and NonDetects as well as on the output of itself (ReplaceValue).
## For further details, see the vignettes in RTqPCR package.

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