readBGX {beadarray} | R Documentation

## Read Illumina .bgx file into R

### Description

Reads in an unzipped Illumina .bgx file, which provides further information on each bead type, including the controls.

### Usage

    readBGX(filename, path=".", sep="\t", quote="", header=TRUE,
               probeStart="\\[Probes\\]", controlStart="\\[Controls\\]", ...)

### Arguments

`filename` | character vector specifying name of unzipped bgx file
`path` | character string specifying the location of the bgx file
`sep` | separator character (default is tab, `"\t"`)
`quote` | character string specifying the quoting characters (disabled by default with `quote=""`). See `scan` for further information.
`header` | logical, TRUE if the bgx file has a header, FALSE otherwise
`probeStart` | character string, below which the information for the beads of interest appear. Default value is "\[Probes\]"
`controlStart` | character string, below which the information for the control beads appear. Default value is "\[Controls\]"
`...` | further arguments to `read.table`

### Details

The .bgx file is a zip file which contains information about each probe on an expression BeadArray.

To read in the file, you first need to unzip it. To do this, replace the .bgx extension with .zip (for example rename `HumanRef-8_V2_0_R0_11223162_A.bgx` as `HumanRef-8_V2_0_R0_11223162_A.zip`) and then unzip this file (which should leave one file `HumanRef-8_V2_0_R0_11223162_A` for our example). The unzipped file is tab delimited file and should be readable using `readBGX`. At present this should work for Human and Rat expression arrays. For Mouse arrays, the .bgx has a more complicated structure.

### Value

`data.frame` containing information about each bead type (probe sequence, ID, control status, etc)

### Author(s)

Matt Ritchie

### Examples

    #human8bgx = readBGX("HumanRef-8_V2_0_R0_11223162_A", fill=TRUE)
    #colnames(human8bgx)
    #summary(human8bgx$Status)
    #human6bgx = readBGX("HumanWG-6_V2_0_R0_11223189_A", fill=TRUE)
    #ratbgx = readBGX("RatRef-12_V1_0_R0_11222119_A", fill=TRUE)

[Package beadarray version 1.12.1 Index]