beadarrayMSV: Analysis of Illumina BeadArray SNP data including MSV markers

Imports bead-summary data from Illumina scanner. Pre-processes using a suite of optional normalizations and transformations. Clusters and automatically calls genotypes, critically able to handle markers in duplicated regions of the genome (multisite variants; MSVs). Interactive clustering if needed. MSVs with variation in both paralogs may be resolved and mapped to their respective chromosomes. Quality control including pedigree checking and visual assessment of clusters. Too large data-sets are handled by working on smaller subsets of the data in sequence.

Version: 1.1.0
Depends: R (≥ 2.10.0), Biobase (≥ 2.5.5), methods, geneplotter
Imports: rggobi, limma
Published: 2011-02-21
Author: Lars Gidskehaug
Maintainer: Lars Gidskehaug <lg at camo.no>
License: GPL-2 | GPL-3 [expanded from: GPL (≥ 2)]
NeedsCompilation: no
SystemRequirements: GGobi
Citation: beadarrayMSV citation info
Materials: ChangeLog
CRAN checks: beadarrayMSV results

Downloads:

Reference manual: beadarrayMSV.pdf
Package source: beadarrayMSV_1.1.0.tar.gz
OS X binary: not available, see check log.
Windows binary: beadarrayMSV_1.1.0.zip
Old sources: beadarrayMSV archive