Hi all,
I would like to get genotype information from HapMap project. Hence, I am
using snpMatrix's read.Hapmap.data, but when i try to get genotype
information, it converts to numerical code form. hence can somebody please
let me know how to get genotype information as it is in the HapMap file?

> library(snpMatrix)
> chr3_CEU <-
read.HapMap.data("file://genotypes_chr3_CEU_r27_nr.b36_fwd.txt")
Reading 174 samples
current line [0] : rs9755941 C/T chr3 3...
current line [20000] : rs34867 C/T chr3 104...
current line [40000] : rs7644151 A/T chr3 2...
current line [60000] : rs7632008 C/T chr3 3...
current line [80000] : rs403286 A/G chr3 55...
current line [100000] : rs1459920 C/T chr3 6...
current line [120000] : rs1384419 A/G chr3 8...
current line [140000] : rs9811293 C/T chr3 1...
current line [160000] : rs10470402 C/T chr3 ...
current line [180000] : rs17373504 C/T chr3 ...
current line [200000] : rs7611580 A/G chr3 1...
current line [220000] : rs695907 C/G chr3 16...
current line [240000] : rs4854927 C/T chr3 1...
last line [259411] : rs3950775 A/C chr3 1...
EOF reached after 259412 snps
 ...conversion complete...

> chr6_CEU$snp.data[,"rs2274459"]
Autosomal snp(s):
NA06984 NA06985 NA06986 NA06989 NA06991 NA06993 NA06994 NA06995 NA06997
NA07000
  "B/B"   "B/B"   "A/B"   "B/B"   "B/B"   "B/B"   "B/B"   "A/B"   "B/B"
"B/B"
NA07014 NA07019 NA07022 NA07029 NA07031 NA07034 NA07037 NA07045 NA07048
NA07051
  "B/B"      ""   "B/B"   "B/B"   "B/B"      ""   "A/B"   "B/B"      ""
"B/B"
NA07055 NA07056 NA07345 NA07346 NA07347 NA07348 NA07349 NA07357 NA07435
NA10830
  "B/B"   "B/B"   "B/B"   "B/B"   "B/B"   "B/B"   "B/B"   "B/B"   "A/A"
"A/B"
NA10831 NA10835 NA10836 NA10837 NA10838 NA10839 NA10840 NA10843 NA10845
NA10846
  "A/B"   "B/B"   "B/B"   "B/B"   "B/B"   "B/B"   "B/B"   "B/B"   "B/B"
"B/B"
NA10847 NA10850 NA10851 NA10852 NA10853 NA10854 NA10855 NA10856 NA10857
NA10859
  "B/B"   "B/B"      ""   "A/B"   "B/B"   "B/B"   "B/B"   "B/B"      ""
"A/B"
NA10860 NA10861 NA10863 NA10864 NA10865 NA11829 NA11830 NA11831 NA11832
NA11839
     ""   "A/B"   "B/B"   "B/B"   "B/B"   "B/B"   "A/B"   "B/B"   "B/B"
"B/B"

> rs2274459_CEU<-as.vector(chr6_CEU$snp.data[,"rs2274459"])
> rs2274459_CEU
  [1] 03 03 02 03 03 03 03 02 03 03 03 00 03 03 03 00 02 03 00 03 03 03 03
03 03
 [26] 03 03 03 01 02 02 03 03 03 03 03 03 03 03 03 03 03 00 02 03 03 03 03
00 02
 [51] 00 02 03 03 03 03 02 03 03 03 03 03 02 03 03 03 03 03 03 03 02 03 03
03 03
 [76] 03 03 02 03 00 03 03 03 03 02 03 03 03 02 03 03 02 03 03 00 03 02 03
03 03
[101] 03 03 03 03 02 03 03 03 03 02 03 02 03 03 03 03 03 02 02 02 03 03 02
03 03
[126] 03 03 00 02 03 03 03 03 03 03 03 02 02 03 01 03 03 03 03 03 03 02 03
03 03
[151] 03 03 03 03 03 03 03 03 03 03 03 03 03 03 03 03 03 03 03 03 03 02 03
02

Regards,
mlsc

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