Mapping250K_Nsp {SNPMaP.cdm} | R Documentation |
A SNPMaP
cdm
for the Affymetrix Mapping250K_Nsp
genotyping microarray that forms a 500K set with the Mapping250K_Sty.
Mapping250K_Nsp
The format is:
List of 2
$ six.probes:List of 2
..$ perfect : int [1:252960, 1:12] 78152 2167382 2284272 2931842 548588 5440644 2799720 3330902 5113224 3410564 ...
.. ..- attr(*, "dimnames")=List of 2
.. .. ..$ : chr [1:252960] "SNP_A-1780520" "SNP_A-1780618" "SNP_A-1780632" "SNP_A-1780654" ...
.. .. ..$ : chr [1:12] "pma1" "pma2" "pma3" "pma4" ...
..$ mismatch: int [1:252960, 1:12] 78153 2167383 2284273 2931843 548589 5440645 2799721 3330903 5113225 3410565 ...
.. ..- attr(*, "dimnames")=List of 2
.. .. ..$ : chr [1:252960] "SNP_A-1780520" "SNP_A-1780618" "SNP_A-1780632" "SNP_A-1780654" ...
.. .. ..$ : chr [1:12] "mma1" "mma2" "mma3" "mma4" ...
$ ten.probes:List of 2
..$ perfect : int [1:9304, 1:20] 5461834 5808782 1479170 3088726 2972016 3253158 6375046 1861456 6019908 938352 ...
.. ..- attr(*, "dimnames")=List of 2
.. .. ..$ : chr [1:9304] "SNP_A-4192498" "SNP_A-4192909" "SNP_A-4192918" "SNP_A-4192955" ...
.. .. ..$ : chr [1:20] "pma1" "pma2" "pma3" "pma4" ...
..$ mismatch: int [1:9304, 1:20] 5461835 5808783 1479171 3088727 2972017 3253159 6375047 1861457 6019909 938353 ...
.. ..- attr(*, "dimnames")=List of 2
.. .. ..$ : chr [1:9304] "SNP_A-4192498" "SNP_A-4192909" "SNP_A-4192918" "SNP_A-4192955" ...
.. .. ..$ : chr [1:20] "mma1" "mma2" "mma3" "mma4" ...
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 Mapping250K_Nsp cdm
inludes mismatch probes as well as perfect match probes and has two
sets
:
The first comprises those 252960 probesets with six quartets, while the second comprises the 9304
probesets with ten 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()
. The mismatch probes are extracted by specifying useMM=TRUE
.