Mapping250K_Sty {SNPMaP.cdm} | R Documentation |
A SNPMaP
cdm
for the Affymetrix Mapping250K_Sty
genotyping microarray that forms a 500K set with the Mapping250K_Nsp.
Mapping250K_Sty
The format is:
List of 2
$ six.probes:List of 2
..$ perfect : int [1:195567, 1:12] 3110922 763382 679536 1173994 2062218 1863554 6463496 531018 3433740 508600 ...
.. ..- attr(*, "dimnames")=List of 2
.. .. ..$ : chr [1:195567] "SNP_A-1855402" "SNP_A-4249904" "SNP_A-2174835" "SNP_A-1880271" ...
.. .. ..$ : chr [1:12] "pma1" "pma2" "pma3" "pma4" ...
..$ mismatch: int [1:195567, 1:12] 3110923 763383 679537 1173995 2062219 1863555 6463497 531019 3433741 508601 ...
.. ..- attr(*, "dimnames")=List of 2
.. .. ..$ : chr [1:195567] "SNP_A-1855402" "SNP_A-4249904" "SNP_A-2174835" "SNP_A-1880271" ...
.. .. ..$ : chr [1:12] "mma1" "mma2" "mma3" "mma4" ...
$ ten.probes:List of 2
..$ perfect : int [1:42737, 1:20] 1979704 3466744 6515338 457896 1439108 4471518 1145816 739218 4053004 5022546 ...
.. ..- attr(*, "dimnames")=List of 2
.. .. ..$ : chr [1:42737] "SNP_A-4246731" "SNP_A-4247531" "SNP_A-4289595" "SNP_A-4258429" ...
.. .. ..$ : chr [1:20] "pma1" "pma2" "pma3" "pma4" ...
..$ mismatch: int [1:42737, 1:20] 1979705 3466745 6515339 457897 1439109 4471519 1145817 739219 4053005 5022547 ...
.. ..- attr(*, "dimnames")=List of 2
.. .. ..$ : chr [1:42737] "SNP_A-4246731" "SNP_A-4247531" "SNP_A-4289595" "SNP_A-4258429" ...
.. .. ..$ : 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_Sty cdm
inludes mismatch probes as well as perfect match probes and has two
sets
:
The first comprises those 195567 probesets with six quartets, while the second comprises the 42737
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
.