read.Mx3005P: To read in the raw fluorescent data of Mx3005P (Agilent)...

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

Description

Function read.Mx3005P reads in txt files of raw fluorescent data of Mx3005P RT -qPCR and uses the data to populate an object of class "RTqPCRBatch".

Usage

read.Mx3005P(file, colNames = c("mxpSegment", "Ramp/Plateaue",
  "Ramp/Plateaue#", "Well", "Dye", "Cycle#", "Fluorescence", "Temperature"),
  cycleThreshold = 45, fileType = "txt", skip = 1, header = TRUE,
  sep = "\t", quote = "\"", dec = ".", fill = TRUE,
  comment.char = "")

Arguments

file	the name of the file to read in.
colNames	a character vector of names to be assumed for the columns.
cycleThreshold	maximum number of cycles which will be read in.
fileType	the type of the file.
skip	an integer: the number of lines of the data file to skip before beginning to read data.
header	a logical value indicating whether the file contains the names of the variables as its first line. If missing, the value is determined from the file format: header is set to TRUE if and only if the first row contains one fewer field than the number of columns.
sep	the field separator character. Values on each line of the file are separated by this character. See read.table.
quote	the set of quoting characters. To disable quoting altogether, use quote = "". See scan for the behaviour on quotes embedded in quotes. Quoting is only considered for columns read as character, which is all of them unless colClasses is specified.
dec	the character used in the file for decimal points.
fill	logical. If TRUE then in case the rows have unequal length, blank fields are implicitly added. See read.table.
comment.char	character: a character vector of length one containing a single character or an empty string. Use "" to turn off the interpretation of comments altogether.
...	other parameters to be passed to downstream methods.

Details

Allows the user to read in qPCR raw fluorescence data from Mx3005P RT-qPCR which has been exported to a txt-file, alongside phenotypic data. More details on how to read in raw fluorescence data from RT-qPCR or Light Cycler in the RTqPCR package vignette.

Value

object of Class "RTqPCRBatch" with exprs slots.

Author(s)

Navneet Phogat, Matthias Kohl, [e-mail]

Examples

path <- system.file("exData", package = "RTqPCR")
Mx3005P.example <- file.path(path, "Mx3005P_Example.txt")
cycData <- read.Mx3005P(Mx3005P.example)
cycData[1:5] ##to visualise the first 5 cycdata and for all data remove [1:5] from the code
featureData(cycData)  ## to visualise the overview of the featureData (feature information of data) 
fData(cycData)[1:5] ## To visualise the content of the first five featureData
## fData(cycData)   To visualise content of all featureData
phenoData(cycData) ## To visualise the overview of phenoData (phenotypic information of data)
pData(cycData)[1:5] ## To visualise the content of the first five phenoData
## pData(cycData) To visualise the content of all phenoData

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