GenomeWideSNP_6 {SNPMaP.cdm} | R Documentation |
A SNPMaP
cdm
for the Affymetrix GenomeWideSNP_6
genotyping microarray.
GenomeWideSNP_6
The format is:
List of 2
$ three.probes:List of 1
..$ perfect: int [1:796045, 1:6] 5273360 4463256 2883438 810524 3933238 3961968 3158564 394894 4680958 4119394 ...
.. ..- attr(*, "dimnames")=List of 2
.. .. ..$ : chr [1:796045] "SNP_A-2131660" "SNP_A-1967418" "SNP_A-1969580" "SNP_A-4263484" ...
.. .. ..$ : chr [1:6] "pma1" "pma2" "pma3" "pmb1" ...
$ four.probes :List of 1
..$ perfect: int [1:110555, 1:8] 2839656 632482 4786064 1551942 5246520 672608 501298 2752888 6755706 2368568 ...
.. ..- attr(*, "dimnames")=List of 2
.. .. ..$ : chr [1:110555] "SNP_A-4268887" "SNP_A-2006248" "SNP_A-2010253" "SNP_A-2017872" ...
.. .. ..$ : chr [1:8] "pma1" "pma2" "pma3" "pma4" ...
The cdm
is used to identify the probesets in the 'raw' SNPMaP
object derived from the
microarray CELs, achieving a similar function to an
Affymetrix CDF file, but faster because it is held in memory once loaded. The GenomeWideSNP_6 cdm
has has two sets
:
The first comprises those 796045 probesets with three quartets, while the second comprises the 110555
probesets with four quartets. These are reached by specifying set
1 or 2 respectively in a call
to snpmap()
. Alternatively, both sets can be read at once using
msnpmap()
.