readBGX {beadarray} | R Documentation |
Reads in an unzipped Illumina .bgx file, which provides further information on each bead type, including the controls.
readBGX(filename, path=".", sep="\t", quote="", header=TRUE, probeStart="\[Probes\]", controlStart="\[Controls\]", ...)
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 |
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.
data.frame
containing information about each bead type (probe
sequence, ID, control status, etc)
Matt Ritchie
#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)