Description Details Author(s) References
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
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
.
Lars Gidskehaug
Maintainer: Lars Gidskehaug lg@camo.no
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
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