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 1.10.0 Index]