read.RTqPCR: To read in the raw fluorescent data of LC480 light cycler and...

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

Description

Function read.RTqPCR reads in the raw fluorescent data of LC480 light cycler and Mx3005P RT-qPCR and use the data to populate an object of class "RTqPCRBatch".

Usage

read.RTqPCR(file, PCRtype, ...)

Arguments

file	the name of the file to read in.
PCRtype	the type of RT-qPCRs ("LC480" or "Mx3005P") whose file is to read in.
...	Other parameters to be passed to downstream methods.

Details

Function read.RTqPCR reads in the raw fluorescent data of LC480 light cycler and Mx3005P RTqPCR and is based on functions read.LC480 and read.Mx3005P.

Value

"RTqPCRBatch" object with exprs slots.

Author(s)

Navneet Phogat, Matthias Kohl, [e-mail]

Examples

##To read in the fluorescent data of LC480 light cycler

LC480.example <- file.path(path, "LC480_Example.txt") 
rtData.LC480 <- read.RTqPCR(LC480.example, PCRtype = "LC480")
rtData.LC480 ## to visualise the overview of data
head(exprs(rtData.LC480)) ## to visualise all of the fluorescence data
head(exprs(rtData.LC480[,1:5])) ## to visualise the first five columns of fluorescence data
head(pData(rtData.LC480)) ## to express the phenoData 
head(fData(rtdata.LC480)) ## to express featureData

##To read in the fluorescent data of Mx3005P RT-qPCR

Mx3005P.example <- file.path(path, "Mx3005P_Example.txt") 
rtData.Mx <- read.RTqPCR(Mx3005P.example, PCRtype = "Mx3005P")
rtData.Mx ## to visualise the overview of data
head(exprs(rtData.Mx)) ## to visualise all of the fluorescence data
head(exprs(rtData.Mx[,1:5])) ## to express the first five columns of fluorescence data
head(pData(rtData.Mx)) ## to express the phenoData
head(fData(rtData.Mx)) ## to express the featureData

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