beadarrayMSV-package: beadarrayMSV: Package for analysis of high-throughput...

Description Details Author(s) References

Description

Functions for reading, pre-processing and analyzing Illumina BeadArray data, in particular from the Infinium platforms. Methods for clustering and genotype calling of multisite variancs (MSVs) from polyploid genomes are provided. Paralogs may be resolved and mapped to individual chromosomes

Details

Package: beadarrayMSV
Type: Package
Version: 1.1
Date: 2011-02-20
License: GPL (>=2)
LazyLoad: yes
LazyData: no
Depends: R (>= 2.10.0), Biobase (>= 2.5.5), methods, geneplotter
Imports: rggobi, limma
SystemRequirements: GGobi

Two classes, "BeadSetIllumina" and "AlleleSetIllumina", are defined for holding and working with genetic data.

Illumina BeadArray summary-data are loaded using the function readBeadSummaryOutput, and pre-processed using preprocessBeadSet.

Automatic clustering and genotype calling is performed using callGenotypes, and validated using validateCallsPedigree and plotGenotypes.

Manual clustering with callGenotypes.interactive, which benefits from the interactive graphics package rggobi. Often used in combination with assignToAlleleSet.

Reading and writing data from and to files with the functions createAlleleSetFromFiles and writeAlleleSet.

For splitting MSV-5 markers into individual paralogs and assigning them to chromosomes, use assignParalogues.

Author(s)

Lars Gidskehaug

Maintainer: Lars Gidskehaug [email protected]

References

L. Gidskehaug, M. Kent, B. J. Hayes, and S. Lien. (2011) Genotype calling and mapping of multisite variants using an Atlantic salmon iSelect SNP-array. Bioinformatics, 27(3):303-310


beadarrayMSV documentation built on May 29, 2017, 9:07 a.m.