readLC480: Read in raw qPCR data of Light Cycler 480
In ReadqPCR: Read qPCR data

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

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

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 = "")

`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.

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

Object of class "CyclesSet".

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

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.

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

  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)

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

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