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

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

View source: R/readqPCRData.R

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

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

`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

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

Object of class "qPCRBatch".

James Perkins jimrperkins@gmail.com

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.

ExpressionSet-class

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  path <- system.file("exData", package = "ReadqPCR")
  qPCR.example <- file.path(path, "qPCR.example.txt")
  qPCRBatch.qPCR <- read.qPCR(qPCR.example)

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'
Warning message:
In read.qPCR(qPCR.example) :
  Incompatible phenoData object. Created a new one using sample name data derived from raw data.