readLC480: Read in raw qPCR data of Light Cycler 480

Description Usage Arguments Details Value Author(s) References See Also Examples

Description

Reads in raw qPCR data of Light Cycler 480 and uses the data to populate an object of class "CyclesSet".

Usage

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read.LC480(file, colNames = c("Sample position", "Sample name",
                              "Program number", "Segment number", 
                              "Cycle number", "Acquisition time", 
                              "Acquisition temperature", 
                              "Fluorescence data"),
           cycleThreshold = 45, fileType = "txt", skip = 1,
           header = TRUE, sep = "\t", quote = "\"", dec = ".",
           fill = TRUE, comment.char = "")

Arguments

file

the name of the file to be 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

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. If sep = "" (the default for read.table) the separator is ‘white space’, that is one or more spaces, tabs, newlines or carriage returns.

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.

Details

Allows the user to read in qPCR fluorescence data from Light Cycler 480 which has been exported to a txt-file, alongside phenotypic data.

Value

Object of class "CyclesSet".

Author(s)

Nor Izayu Abdul Rahman, Matthias Kohl Matthias.Kohl@stamats.de

References

Perkins, JR, Dawes, JM, McMahon, SB, Bennett, DL, Orengo, C, Kohl, M (2012). ReadqPCR and NormqPCR: R packages for the reading, quality checking and normalisation of RT-qPCR quantification cycle (Cq) data. BMC Genomics, 13, 1:296.

See Also

read.table

read.LC480SampleInfo for reading in sample information of qPCR data from Light Cycler and produce an object of Class "CyclesSet".

merge for merging the phenodata from read.LC480 and read.LC480SampleInfo and produce an object of Class "CyclesSet".

read.qPCR and read.taqman for reading in the RT-qPCR data consisting of Cq values.

eSet, CyclesSet-class

Examples

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  path <- system.file("exData", package = "ReadqPCR")
  LC480.example <- file.path(path, "LC480_Example.txt")

  ## Read in the raw qPCR data from file "LC480_Example.txt"
  ## with maximum cycle to be read in the values is 45 (default).
  cycData <- read.LC480(file = LC480.example)
  
  ## Read in the data from file "LC480_Example.txt" 
  ## with maximum cycle to be read in the values is 50.
  rawdata <- read.LC480(file=LC480.example, cycleThreshold=50)

Example output

Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: affy
Warning message:
In read.dcf(con) :
  URL 'http://bioconductor.org/BiocInstaller.dcf': status was 'Couldn't resolve host name'

ReadqPCR documentation built on Nov. 8, 2020, 6:52 p.m.