readQC {beadarray} | R Documentation

## Read Illumina quality control information

### Description

Reads the standard format of Illumina quality control information and produces diagnostic plots

### Usage

    readQC(file, columns = list(exprs = "AVG_Signal", NoBeads = "Avg_NBEADS", Detection="Detection", se.exprs="BEAD_STDERR", Narrays="NARRAYS", arrayStDev = "ARRAY_STDEV", controlID = "ProbeID", controlType="TargetID"),sep="\t",skip=7,header=T)

### Arguments

`file` | name of file containing qc information
`columns` | a vector of column names to read from the file
`skip` | number of lines of header information to ignore in the file
`header` | if TRUE the column names in the file are read
`sep` | a character string for the file separator

### Details

The format of the quality control files differs slightly between BeadStudio versions 1 and 2. Version 1 of the software gives one averaged value for each control type, whereas version 2 gives summarised values for each control of a particular type. The user does not have to know the version of BeadStudio used to generate the file.

Once read in, the quality control information can be very useful for diagnostic purposes.

### Value

readQC produces an assayData object with list items defined by the columns parameter.

### Author(s)

Mark Dunning

### Examples

    ##Code to read the example quality control file included with the
    #package.
    #QC = readQC("raw_data_qcinfo.csv", sep=",", skip=7, columns=list(exprs="AVG.Signal", se.exprs="SeqVAR"))

    #the average expression of each control can then be accessed by the $ operator

    #QC$exprs

[Package beadarray version 1.6.0 Index]