readQC {beadarray} | R Documentation

## Read Illumina control intensities

### Description

Reads the standard format of Illumina control intensities output by BeadStudio

### Usage

    readQC(file, sep="\t", skip=8, controlID = "ProbeID", columns = list(exprs = "AVG_Signal", se.exprs="BEAD_STDERR", NoBeads = "Avg_NBEADS", Detection="Detection Pval"), dec=".", quote="")

### Arguments

`file` | character string giving the name of the file output by BeadStudio containing the control probe intensities. This file should be either the 'ControlProbeProfile' or 'ControlGeneProfile'.
`sep` | a character string for the file separator
`skip` | number of lines of header information to ignore in the file
`controlID` | character string specifying the column that contains the (unique) control probe IDs
`columns` | a vector of column names to read from the file
`dec` | the character used in the file for decimal points
`quote` | the set of quoting characters (disabled by default)

### Details

The format of the quality control files differs slightly between BeadStudio versions 1 and later versions. This function is able to read in data in either format

Note that if the control identifiers are non-unique, the duplicated rows are removed. This may occur if the 'ControlProbeProfile' is exported from BeadStudio and `controlID="TargetID"` is specified (the "ProbeID" column has a unique identifier in the 'ControlProbeProfile', whereas the "TargetID" may not, as multiple beads can be of the same type).

Once read in, the control intensities can be used for quality assessment purposes.

### Value

`readQC` produces an `assayData` object with a list of items defined by the `columns` parameter. The row names of each matrix are given by the `controlID` argument .

### Author(s)

Mark Dunning

### Examples

    ##Code to read the example quality control file included with the
    #package.
    #QC = readQC("ControlGeneProfile.txt", controlID="TargetID")
    #the average expression of each control can then be accessed by the $ operator
    #QC$exprs

[Package beadarray version 1.12.1 Index]