NonDetects: Remove the non-detects ('NA') of Cq and amplification...

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

Description

Remove the non detects (NA) of Cq values and amplification efficiencies within the replicates in the object of class "RTqPCRBatch" on the basis of statistical concepts of mean and median.

Usage

## S4 method for signature 'RTqPCRBatch'
NonDetects(RTqPCRBatch, Calc = "Mean", ...)

Arguments

RTqPCRBatch	Object of class RTqPCRBatch. It can be output of CqValues or ReplaceValue or NonDetects or ReplaceAboveCutOff functions.
Calc	Which method to be used out of "Mean" or "Median". Default is "Mean".
...	Other parameters to be passed to downstream methods.

Details

See the 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 non-detects (NA) within replicates, based on the concept of mean
## default method is mean.

Cqeffs.NA.mean <- NonDetects(Cqeffs.LC480)
Cqeffs.NA.mean ## To see the overview of data
exprs(Cqeffs.NA.mean)[1:5]  ## to visualise the first five Cq values 
effs(Cqeffs.NA.mean)[1:5]  ## to visualise the first five amplification efficiencies
exprs(Cqeffs.NA.mean)  ## to visualise all Cq values
effs(Cqeffs.NA.mean)   ## to visualise all amplification efficiencies

## Replace the non-detects (NA) within replicates, based on the concept of median

Cqeffs.NA.med <- NonDetects(Cqeffs.LC480, Calc = "Median")
Cqeffs.NA.med ## To see the overview of data
exprs(Cqeffs.NA.med)[1:5]  ## to visualise the first five Cq values 
effs(Cqeffs.NA.med)[1:5]  ## to visualise the first five amplification efficiencies
exprs(Cqeffs.NA.med)  ## to visualise all Cq values
effs(Cqeffs.NA.med)   ## to visualise all amplification efficiencies

## The function NonDetects can also be implemented on the outputs of other functions ReplaceValue, 
## ReplaceAboveCutOff and NonDetects. For detail, see the vignettes in RTqPCR package.  

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