SNPMaP.cdm-package {SNPMaP.cdm} | R Documentation |
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.
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/.
This distribution of the SNPMaP.cdm
package includes cdm
matrices for the following arrays:
Mapping250K_Sty
Mapping250K_Nsp
GenomeWideSNP_5
GenomeWideSNP_6
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.
Oliver SP Davis and Leo C Schalkwyk
Maintainer: Oliver SP Davis snpmap@iop.kcl.ac.uk
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
The SNPMaP
package.