import.illumina.bgx: Import an Illumina microarray manifest file.

In drmjc/microarrays: A collection of microarray and genomic helper code.

Description

Illumina microarray manifest files describe the contents of each microarray, including the probe names and sequences among many other things. You can download them from [1] or [2]. You should download the text versions of these files, unzip them and import using this function. You can either import the probe information,or the control information.

Usage

  import.illumina.bgx(file, what = c("probes", "controls"))

Arguments

file	the path to the Illimina BGX file
what	what probes to import? one of “probes” or “controls”

Value

a data.frame representation of the probes from a BGX file.

Note

This seems like a way to unzip BGX manifest files which i don't remember being possible:
if the file ends in zip, then unzip it. then unzip the bgx file using gunzip -S .bgx xxxxx, then rename it to end with .bgx again & import it using this function.

Author(s)

Mark Cowley, 2008-10-23

References

[1] http://www.switchtoi.com/annotationfiles.ilmn [2] http://www.switchtoi.com/annotationprevfiles.ilmn

drmjc/microarrays documentation built on May 15, 2019, 2:26 p.m.