SNPMaP.cdm-package {SNPMaP.cdm}R Documentation

Annotation for SNP Microarrays and Pooling in R

Description

Pooling DNA on SNP microarrays is a cost-effective way to carry out genome-wide association studies for heritable disorders or traits. The SNPMaP package provides formal SNPMaP objects and methods in R as a base for these analyses using Affymetrix genotyping arrays. The SNPMaP.cdm package provides cdm objects for the SNPMaP package.

Details

Package: SNPMaP.cdm
Type: Package
Version: 1.0.0
Date: 2008-06-24
License: GPL (>= 3)

Once the CEL files of the microarrays used in a SNPMaP study have been read into a 'raw' format SNPMaP object, a cdm matrix is used to identify the probesets, achieving a similar function to an Affymetrix CDF file, but faster because it is held in memory once loaded. Each cdm object may comprise several matrices, each referring to a different 'set' of probes. For example, the GenomeWideSNP_6 cdm contains two sets: one with three probes per SNP, the other with four probes per SNP. The cdm objects for older arrays may contain corresponding sets of mismatch probes. The SNPMaP package is an evolution of the scripts referred to in Meaburn et al (2006) and is described in Davis, Plomin and Schalkwyk (submitted for publication); please cite this paper if you find the package useful. Additional supporting material is available at http://sgdp.iop.kcl.ac.uk/snpmap/.

Array types

This distribution of the SNPMaP.cdm package includes cdm matrices for the following arrays:
Mapping250K_Sty
Mapping250K_Nsp
GenomeWideSNP_5
GenomeWideSNP_6

Future work

Future releases of the package will build on the range of chips covered, and custom cdms will be made available on the SNPMaP Web site.

Author(s)

Oliver SP Davis and Leo C Schalkwyk

Maintainer: Oliver SP Davis snpmap@iop.kcl.ac.uk

References

Davis, OSP, Plomin, R, and Schalkwyk, LC. (submitted for publication) The SNPMaP package for R: A framework for genome-wide association using DNA pooling on microarrays.

Meaburn E, Butcher LM, Schalkwyk LC, and Plomin R. (2006) Genotyping pooled DNA using 100K SNP microarrays: a step towards genomewide association scans. Nucleic Acids Research, 34(4):e28. http://dx.doi.org/10.1093/nar/gnj027

See Also

The SNPMaP package.


[Package SNPMaP.cdm version 1.0.0 Index]