read.taqman: Read Taqman qPCR data and produce a qPCRBatch

In jimrperkins/ReadqPCR: Read qPCR data

Description

Reads Taqman RT-qPCR data and uses the data to populate an object of class "qPCRBatch".

Usage

read.taqman(...,
           filenames = character(0),
           phenoData = new("AnnotatedDataFrame"),
           notes = "", 
           verbose = FALSE)

Arguments

...	file names separated by comma.
filenames	file names in a character vector.
phenoData	an AnnotatedDataFrame object, a character of length one, or a data.frame.
notes	notes.
verbose	verbosity flag. If true more messages are given to the user on the processing steps

Details

Permits the user to read in qPCR Cq value data from an sds output file, alongside phenotypic data and further notes about the data. If phenoData is a data.frame, it is converted to an AnnotatedDataFrame. If it is NULL then a default object of class AnnotatedDataFrame is created, whose pData is a data.frame with rownames being the names of the , and with one column sample with an integer index. More details on how technical replicates are handled in the ReadqPCR package vignette

Value

Object of class "qPCRBatch".

Author(s)

James Perkins [e-mail]

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

ExpressionSet-class

Examples

  path <- system.file("exData", package = "ReadqPCR")
  # read 1 file
  taqman.example <- file.path(path, "example.txt")
  qPCRBatch.taq <- read.taqman(taqman.example)
  # read 2 files
  taqman.example.second.file <- file.path(path, "example2.txt")
  qPCRBatch.taq.two.files <- read.taqman(taqman.example, 
                             taqman.example.second.file)

jimrperkins/ReadqPCR documentation built on March 30, 2020, 10:23 p.m.