ReadqPCR (version 1.18.0)

read.qPCR: Read user formatted qPCR data and produce a qPCRBatch

Description

Reads RT-qPCR data in format specified in the ReadqPCR vignette and uses the data to populate an object of class "qPCRBatch".

Usage

read.qPCR(filename = character(0), phenoData = new("AnnotatedDataFrame"), notes = "", verbose = FALSE)

Arguments

filename

file name (must be formatted as shown in vignette).

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

Value

"qPCRBatch".

Details

Permits the user to read in qPCR Cq value data in a predefined format (more details on this format in the ReadqPCR package vignette), 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 samples, and with one column sample with an integer index. More details on how technical replicates are handled in the ReadqPCR package vignette

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")
  qPCR.example <- file.path(path, "qPCR.example.txt")
  qPCRBatch.qPCR <- read.qPCR(qPCR.example)