Extract a genotype matrix from an object that carries genotype
data. For an LdData, returns the underlying genotype matrix via its
handle (or NULL if no handle is available). For a QtlDataset,
returns the genotype matrix for a selected set of traits or region (see
method documentation for the per-class selection arguments).
Usage
getGenotypes(x, ...)
# S4 method for class 'LdData'
getGenotypes(x, ...)
# S4 method for class 'QtlDataset'
getGenotypes(
x,
traitId = NULL,
region = NULL,
cisWindow = NULL,
samples = NULL,
...
)Arguments
- x
The object to extract from.
- ...
Class-specific selection arguments (e.g.,
traitId,region,cisWindowforQtlDataset).- traitId
Character or
NULL. Molecular trait / feature identifier to select;NULLmatches all traits in the dataset.- region
Character (length 1,
"chr:start-end") orNULL. Restrict variants to this region;NULLuses the full cis window / all regions.- cisWindow
Integer or
NULL. Half-width (bp) of the cis window around the trait;NULLuses the dataset default.- samples
Character vector or
NULL. Restrict to these sample IDs;NULLuses all samples.
Examples
data(qtlDatasetExample)
getGenotypes(qtlDatasetExample)
#> chr22:14560203:A:G chr22:14564328:T:C chr22:14850625:T:G
#> NA06989 0 0 1
#> NA11891 1 1 0
#> NA11843 0 1 0
#> NA12341 0 0 0
#> NA12739 1 1 0
#> NA10850 0 0 1
#> NA06984 1 0 1
#> NA12877 0 1 0
#> NA12275 0 0 1
#> NA06986 0 1 1
#> NA12272 0 0 0
#> NA10845 0 1 0
#> NA10852 0 0 0
#> NA07051 0 0 0
#> NA12400 0 1 1
#> NA12344 0 0 0
#> NA12777 0 0 0
#> NA12287 0 0 1
#> NA10837 0 0 0
#> NA12383 0 0 0
#> NA12340 0 0 1
#> NA12708 0 0 0
#> NA12273 0 0 0
#> NA11892 0 0 1
#> NA12546 0 0 0
#> NA12843 0 0 0
#> NA12766 0 0 0
#> NA12348 0 0 0
#> NA12817 0 0 1
#> NA10840 0 1 0
#> NA06997 0 1 1
#> NA11917 0 0 0
#> NA12718 0 0 0
#> NA12282 0 0 0
#> NA11920 0 0 0
#> NA12776 0 0 1
#> NA12283 0 0 0
#> NA07435 0 1 0
#> NA12828 0 0 1
#> NA07045 0 1 0
#> NA07031 0 0 0
#> NA12336 0 1 0
#> NA07349 0 1 0
#> NA12827 0 1 1
#> NA12375 0 1 0
#> NA12343 0 0 0
#> NA12335 0 0 1
#> NA12778 0 0 0
#> NA12832 0 0 0
#> NA11930 0 1 1
#> NA12890 0 0 0
#> NA07037 1 1 0
#> NA07347 0 0 1
#> NA12829 0 1 0
#> NA12749 1 0 0
#> NA11894 0 0 0
#> NA12286 0 1 1
#> NA10865 1 1 0
#> NA10864 1 0 0
#> NA10853 0 0 1
#> NA11918 0 0 1
#> NA12830 0 1 1
#> NA12818 0 1 0
#> NA10836 0 0 0
#> NA11893 1 0 0
#> NA11919 0 0 0
#> NA12489 1 1 0
#> NA12399 0 0 0
#> NA12413 0 0 0
#> NA10843 0 0 0
#> NA12842 1 1 0
#> NA12347 0 0 0
#> NA07346 1 1 0
#> NA12775 0 0 0
#> NA07014 0 0 0
#> NA12767 0 0 0
#> NA12889 0 1 0
#> NA12386 0 1 0
#> NA06995 0 0 0
#> NA12376 0 1 0
#> NA12342 0 1 0
#> NA12748 1 1 0
#> NA11931 0 1 0
#> NA12045 0 0 0
#> NA12750 1 0 0
#> NA11831 0 0 1
#> NA12146 0 0 0
#> NA11882 0 0 1
#> NA07056 0 1 0
#> NA12707 0 0 0
#> NA12154 1 0 0
#> NA12753 0 0 0
#> NA11839 0 0 0
#> NA10859 0 0 1
#> NA12875 0 1 1
#> NA07348 0 0 0
#> NA12156 0 1 1
#> NA12044 0 0 0
#> NA11992 0 0 0
#> NA11829 0 0 0
#> NA12239 0 0 0
#> NA12762 0 1 0
#> NA12716 0 0 1
#> NA12878 0 0 0
#> NA10856 0 0 0
#> NA12874 0 0 0
#> NA12760 1 0 0
#> NA06985 1 0 0
#> NA12003 0 0 0
#> NA10835 0 1 1
#> NA07022 0 1 1
#> NA12813 0 1 0
#> NA10839 0 0 0
#> NA07055 0 0 0
#> NA12056 0 1 0
#> NA10863 0 0 0
#> NA12145 0 0 0
#> NA12814 0 0 0
#> NA10847 0 0 0
#> NA12006 0 1 0
#> NA12763 0 0 0
#> NA07357 0 0 0
#> NA12144 0 1 1
#> NA10831 0 1 1
#> NA07000 0 1 0
#> NA11832 0 1 0
#> NA06991 0 0 0
#> NA11840 0 0 1
#> NA12802 0 0 0
#> NA12761 1 0 1
#> NA10830 1 0 0
#> NA10855 0 0 1
#> NA06994 0 0 1
#> NA11993 0 1 1
#> NA11995 0 0 0
#> NA12891 0 0 0
#> NA12864 1 1 0
#> NA12751 0 1 0
#> NA10861 1 0 0
#> NA12005 0 0 0
#> NA12234 0 0 0
#> NA07345 0 1 0
#> NA07029 0 1 0
#> NA12892 0 0 0
#> NA12248 0 0 1
#> NA10846 0 1 1
#> NA12801 0 0 0
#> NA12872 1 0 1
#> NA12155 0 0 0
#> NA06993 0 0 0
#> NA11830 0 0 0
#> NA10838 0 0 0
#> NA12249 0 1 1
#> NA12057 1 0 0
#> NA12812 0 1 0
#> NA11881 0 1 0
#> NA11994 1 0 0
#> NA12873 1 1 0
#> NA12815 0 1 0
#> NA12740 0 1 0
#> NA12752 1 0 0
#> NA12043 0 1 0
#> NA12264 0 0 0
#> NA10854 0 0 1
#> NA12865 0 1 1
#> chr22:14870204:T:C chr22:14878387:G:A chr22:14880040:A:G
#> NA06989 0 0.0000000 0
#> NA11891 1 0.0000000 1
#> NA11843 0 0.0000000 0
#> NA12341 1 2.0000000 0
#> NA12739 2 0.0000000 2
#> NA10850 1 1.0000000 1
#> NA06984 1 0.0000000 1
#> NA12877 1 0.0000000 0
#> NA12275 0 1.0000000 0
#> NA06986 0 1.0000000 0
#> NA12272 2 0.0000000 0
#> NA10845 0 1.0000000 0
#> NA10852 0 1.0000000 0
#> NA07051 1 0.0000000 0
#> NA12400 1 1.0000000 0
#> NA12344 0 0.0000000 0
#> NA12777 1 1.0000000 0
#> NA12287 0 1.0000000 0
#> NA10837 1 0.0000000 0
#> NA12383 1 1.0000000 1
#> NA12340 0 0.0000000 0
#> NA12708 0 0.0000000 0
#> NA12273 0 0.0000000 0
#> NA11892 0 1.0000000 0
#> NA12546 0 0.0000000 0
#> NA12843 0 0.0000000 0
#> NA12766 0 0.0000000 0
#> NA12348 1 0.0000000 1
#> NA12817 1 1.0000000 0
#> NA10840 0 1.0000000 0
#> NA06997 0 1.0000000 0
#> NA11917 0 0.0000000 0
#> NA12718 1 1.0000000 0
#> NA12282 1 0.0000000 1
#> NA11920 1 0.0000000 0
#> NA12776 0 0.0000000 0
#> NA12283 0 0.0000000 0
#> NA07435 1 0.0000000 1
#> NA12828 1 0.0000000 1
#> NA07045 0 0.0000000 0
#> NA07031 0 2.0000000 0
#> NA12336 0 0.0000000 0
#> NA07349 0 0.0000000 0
#> NA12827 1 0.3312883 0
#> NA12375 1 0.0000000 1
#> NA12343 0 0.0000000 0
#> NA12335 0 1.0000000 0
#> NA12778 1 1.0000000 0
#> NA12832 1 0.0000000 1
#> NA11930 0 0.0000000 0
#> NA12890 1 0.0000000 1
#> NA07037 1 1.0000000 1
#> NA07347 0 0.0000000 0
#> NA12829 0 0.0000000 0
#> NA12749 2 0.0000000 2
#> NA11894 1 0.0000000 1
#> NA12286 0 1.0000000 0
#> NA10865 1 0.0000000 1
#> NA10864 2 0.0000000 2
#> NA10853 0 0.0000000 0
#> NA11918 0 0.0000000 0
#> NA12830 1 0.0000000 0
#> NA12818 1 0.0000000 0
#> NA10836 1 1.0000000 0
#> NA11893 2 0.0000000 2
#> NA11919 1 1.0000000 1
#> NA12489 2 1.0000000 2
#> NA12399 1 0.0000000 2
#> NA12413 1 0.0000000 1
#> NA10843 1 0.0000000 0
#> NA12842 2 1.0000000 2
#> NA12347 1 1.0000000 0
#> NA07346 1 0.0000000 1
#> NA12775 0 0.0000000 0
#> NA07014 1 1.0000000 0
#> NA12767 1 1.0000000 0
#> NA12889 2 1.0000000 0
#> NA12386 2 1.0000000 1
#> NA06995 1 0.0000000 1
#> NA12376 1 1.0000000 1
#> NA12342 0 0.0000000 0
#> NA12748 1 0.0000000 1
#> NA11931 0 1.0000000 0
#> NA12045 0 0.0000000 0
#> NA12750 1 0.0000000 1
#> NA11831 0 1.0000000 0
#> NA12146 1 1.0000000 0
#> NA11882 0 0.0000000 0
#> NA07056 0 0.0000000 0
#> NA12707 0 0.0000000 0
#> NA12154 2 1.0000000 2
#> NA12753 0 1.0000000 0
#> NA11839 1 1.0000000 0
#> NA10859 0 0.0000000 0
#> NA12875 1 1.0000000 0
#> NA07348 2 1.0000000 0
#> NA12156 0 0.0000000 0
#> NA12044 1 0.0000000 0
#> NA11992 0 0.0000000 0
#> NA11829 1 1.0000000 0
#> NA12239 0 0.0000000 0
#> NA12762 0 1.0000000 0
#> NA12716 0 0.0000000 0
#> NA12878 1 1.0000000 0
#> NA10856 0 1.0000000 0
#> NA12874 1 0.0000000 0
#> NA12760 2 0.0000000 1
#> NA06985 2 1.0000000 1
#> NA12003 0 0.0000000 0
#> NA10835 0 0.0000000 0
#> NA07022 1 1.0000000 0
#> NA12813 0 0.0000000 0
#> NA10839 1 0.0000000 0
#> NA07055 1 0.0000000 0
#> NA12056 2 0.0000000 1
#> NA10863 2 0.0000000 0
#> NA12145 0 0.0000000 0
#> NA12814 0 0.0000000 0
#> NA10847 1 0.0000000 0
#> NA12006 2 0.0000000 0
#> NA12763 0 0.0000000 0
#> NA07357 2 0.0000000 1
#> NA12144 0 0.0000000 0
#> NA10831 0 0.0000000 0
#> NA07000 0 1.0000000 0
#> NA11832 1 0.0000000 0
#> NA06991 1 0.0000000 0
#> NA11840 0 0.0000000 0
#> NA12802 1 0.0000000 1
#> NA12761 1 0.0000000 1
#> NA10830 2 1.0000000 2
#> NA10855 0 0.0000000 0
#> NA06994 1 0.0000000 1
#> NA11993 0 0.0000000 0
#> NA11995 1 0.0000000 0
#> NA12891 1 1.0000000 0
#> NA12864 2 0.0000000 2
#> NA12751 0 0.0000000 0
#> NA10861 1 0.0000000 1
#> NA12005 0 0.0000000 0
#> NA12234 1 1.0000000 0
#> NA07345 1 1.0000000 0
#> NA07029 1 1.0000000 1
#> NA12892 1 0.0000000 0
#> NA12248 0 0.0000000 0
#> NA10846 0 0.0000000 0
#> NA12801 1 0.0000000 0
#> NA12872 1 0.0000000 1
#> NA12155 0 1.0000000 0
#> NA06993 0 0.0000000 0
#> NA11830 0 0.0000000 0
#> NA10838 1 0.0000000 1
#> NA12249 0 0.0000000 0
#> NA12057 2 0.0000000 1
#> NA12812 1 0.0000000 0
#> NA11881 0 0.0000000 0
#> NA11994 2 0.0000000 1
#> NA12873 1 0.0000000 1
#> NA12815 1 0.0000000 1
#> NA12740 1 0.0000000 1
#> NA12752 2 0.0000000 1
#> NA12043 1 0.3312883 0
#> NA12264 1 0.0000000 0
#> NA10854 0 0.0000000 0
#> NA12865 0 1.0000000 0
#> chr22:14884399:T:C chr22:15063831:A:G chr22:15257135:C:G
#> NA06989 0 0 0.0000000
#> NA11891 1 1 1.0000000
#> NA11843 2 0 0.0000000
#> NA12341 0 0 0.0000000
#> NA12739 0 2 0.0000000
#> NA10850 0 0 0.0000000
#> NA06984 1 1 0.0000000
#> NA12877 0 0 0.0000000
#> NA12275 0 0 0.0000000
#> NA06986 0 0 1.0000000
#> NA12272 0 0 0.0000000
#> NA10845 0 0 0.0000000
#> NA10852 0 0 0.0000000
#> NA07051 0 0 0.0000000
#> NA12400 0 0 1.0000000
#> NA12344 0 0 0.0000000
#> NA12777 1 0 0.0000000
#> NA12287 1 0 0.0000000
#> NA10837 0 0 0.1419753
#> NA12383 0 0 0.0000000
#> NA12340 0 0 0.0000000
#> NA12708 1 0 0.0000000
#> NA12273 1 0 0.0000000
#> NA11892 0 0 0.0000000
#> NA12546 1 0 0.0000000
#> NA12843 0 0 1.0000000
#> NA12766 0 0 0.0000000
#> NA12348 0 0 0.0000000
#> NA12817 0 0 1.0000000
#> NA10840 0 1 0.0000000
#> NA06997 1 0 0.1419753
#> NA11917 0 0 0.0000000
#> NA12718 0 0 1.0000000
#> NA12282 1 0 0.0000000
#> NA11920 1 0 0.0000000
#> NA12776 0 0 0.0000000
#> NA12283 0 0 0.0000000
#> NA07435 0 0 0.0000000
#> NA12828 0 0 1.0000000
#> NA07045 1 0 1.0000000
#> NA07031 0 0 1.0000000
#> NA12336 1 0 0.0000000
#> NA07349 0 0 0.0000000
#> NA12827 0 0 1.0000000
#> NA12375 0 0 0.0000000
#> NA12343 0 0 0.0000000
#> NA12335 0 0 0.0000000
#> NA12778 0 0 0.0000000
#> NA12832 0 0 0.0000000
#> NA11930 0 0 0.0000000
#> NA12890 0 1 0.0000000
#> NA07037 0 1 1.0000000
#> NA07347 0 0 0.0000000
#> NA12829 0 0 1.0000000
#> NA12749 0 2 0.0000000
#> NA11894 0 0 0.0000000
#> NA12286 0 1 0.0000000
#> NA10865 0 1 0.0000000
#> NA10864 0 1 0.0000000
#> NA10853 1 0 0.1419753
#> NA11918 0 0 0.0000000
#> NA12830 1 0 0.0000000
#> NA12818 1 0 1.0000000
#> NA10836 1 0 0.0000000
#> NA11893 0 2 0.0000000
#> NA11919 0 0 0.0000000
#> NA12489 0 1 0.0000000
#> NA12399 0 0 0.0000000
#> NA12413 0 0 1.0000000
#> NA10843 1 0 0.0000000
#> NA12842 0 1 0.0000000
#> NA12347 0 0 1.0000000
#> NA07346 0 1 0.0000000
#> NA12775 0 0 0.0000000
#> NA07014 0 0 0.0000000
#> NA12767 0 0 0.0000000
#> NA12889 0 0 0.0000000
#> NA12386 0 0 1.0000000
#> NA06995 0 0 0.0000000
#> NA12376 1 0 0.0000000
#> NA12342 2 0 0.0000000
#> NA12748 0 1 0.0000000
#> NA11931 0 0 0.0000000
#> NA12045 0 0 0.0000000
#> NA12750 0 1 0.0000000
#> NA11831 0 0 0.0000000
#> NA12146 0 0 1.0000000
#> NA11882 1 0 0.0000000
#> NA07056 0 0 0.0000000
#> NA12707 0 0 0.0000000
#> NA12154 1 1 0.0000000
#> NA12753 0 0 0.0000000
#> NA11839 0 0 0.0000000
#> NA10859 2 0 0.0000000
#> NA12875 0 0 0.0000000
#> NA07348 0 0 0.0000000
#> NA12156 0 0 0.0000000
#> NA12044 0 0 0.0000000
#> NA11992 1 0 0.0000000
#> NA11829 1 0 0.0000000
#> NA12239 0 0 0.0000000
#> NA12762 0 0 0.0000000
#> NA12716 0 0 0.0000000
#> NA12878 0 0 0.0000000
#> NA10856 0 0 0.0000000
#> NA12874 1 0 0.0000000
#> NA12760 0 1 0.0000000
#> NA06985 0 1 0.0000000
#> NA12003 0 0 0.0000000
#> NA10835 0 0 0.0000000
#> NA07022 0 0 0.0000000
#> NA12813 1 0 0.0000000
#> NA10839 0 0 0.0000000
#> NA07055 0 0 0.0000000
#> NA12056 0 0 0.0000000
#> NA10863 0 0 0.0000000
#> NA12145 0 0 0.0000000
#> NA12814 0 0 0.0000000
#> NA10847 0 0 1.0000000
#> NA12006 0 0 0.0000000
#> NA12763 0 0 0.0000000
#> NA07357 0 0 0.0000000
#> NA12144 0 0 0.0000000
#> NA10831 0 0 0.0000000
#> NA07000 0 0 0.0000000
#> NA11832 2 0 0.0000000
#> NA06991 0 0 0.0000000
#> NA11840 0 0 0.0000000
#> NA12802 0 1 0.0000000
#> NA12761 2 1 0.0000000
#> NA10830 0 1 0.0000000
#> NA10855 1 0 0.0000000
#> NA06994 1 1 0.0000000
#> NA11993 0 0 0.0000000
#> NA11995 1 0 0.0000000
#> NA12891 0 0 0.0000000
#> NA12864 0 2 0.0000000
#> NA12751 0 0 0.0000000
#> NA10861 1 1 0.0000000
#> NA12005 0 0 0.0000000
#> NA12234 0 0 0.0000000
#> NA07345 0 0 0.0000000
#> NA07029 1 1 0.0000000
#> NA12892 0 0 0.0000000
#> NA12248 0 0 0.0000000
#> NA10846 0 0 0.0000000
#> NA12801 1 0 1.0000000
#> NA12872 0 1 0.0000000
#> NA12155 0 0 0.0000000
#> NA06993 0 0 0.0000000
#> NA11830 1 0 0.0000000
#> NA10838 0 0 0.0000000
#> NA12249 1 0 0.0000000
#> NA12057 0 1 0.0000000
#> NA12812 1 0 1.0000000
#> NA11881 1 0 0.0000000
#> NA11994 0 1 0.0000000
#> NA12873 0 1 1.0000000
#> NA12815 0 1 0.0000000
#> NA12740 0 1 0.0000000
#> NA12752 1 1 0.0000000
#> NA12043 0 0 2.0000000
#> NA12264 0 0 0.0000000
#> NA10854 0 0 0.0000000
#> NA12865 0 0 0.0000000
#> chr22:15266873:A:G chr22:15268900:C:G chr22:15298335:T:C
#> NA06989 1.00000 1.0000000 0.0000000
#> NA11891 1.00000 1.0000000 1.0000000
#> NA11843 0.00000 0.0000000 0.0000000
#> NA12341 2.00000 2.0000000 2.0000000
#> NA12739 0.00000 0.0000000 1.0000000
#> NA10850 1.00000 1.0000000 1.0000000
#> NA06984 0.00000 0.0000000 0.0000000
#> NA12877 0.00000 0.0000000 2.0000000
#> NA12275 1.00000 1.0000000 1.0000000
#> NA06986 1.00000 1.0000000 0.0000000
#> NA12272 1.00000 1.0000000 1.0000000
#> NA10845 0.00000 0.0000000 1.0000000
#> NA10852 0.00000 0.0000000 2.0000000
#> NA07051 1.00000 1.0000000 0.0000000
#> NA12400 0.00000 0.0000000 0.0000000
#> NA12344 0.00000 0.0000000 1.0000000
#> NA12777 1.00000 1.0000000 1.0000000
#> NA12287 0.00000 0.0000000 0.0000000
#> NA10837 2.00000 0.5925926 0.0000000
#> NA12383 1.00000 1.0000000 1.0000000
#> NA12340 0.00000 1.0000000 2.0000000
#> NA12708 1.00000 1.0000000 1.0000000
#> NA12273 1.00000 0.5925926 1.0000000
#> NA11892 0.00000 0.0000000 1.0000000
#> NA12546 0.00000 0.0000000 0.0000000
#> NA12843 0.00000 0.0000000 0.0000000
#> NA12766 0.00000 0.0000000 0.0000000
#> NA12348 1.00000 1.0000000 1.0000000
#> NA12817 1.00000 1.0000000 1.0000000
#> NA10840 0.00000 0.0000000 0.0000000
#> NA06997 1.00000 1.0000000 1.0000000
#> NA11917 1.00000 1.0000000 0.0000000
#> NA12718 0.00000 0.0000000 0.0000000
#> NA12282 0.00000 0.0000000 0.0000000
#> NA11920 0.00000 0.0000000 1.0000000
#> NA12776 0.00000 0.0000000 0.0000000
#> NA12283 0.00000 0.0000000 1.0000000
#> NA07435 1.00000 1.0000000 1.0000000
#> NA12828 0.00000 0.0000000 1.0000000
#> NA07045 0.00000 0.0000000 1.0000000
#> NA07031 0.00000 0.0000000 1.0000000
#> NA12336 0.00000 0.0000000 0.0000000
#> NA07349 2.00000 2.0000000 1.0000000
#> NA12827 1.00000 1.0000000 1.0000000
#> NA12375 0.00000 0.0000000 1.0000000
#> NA12343 0.00000 0.0000000 0.0000000
#> NA12335 1.00000 2.0000000 1.0000000
#> NA12778 1.00000 1.0000000 2.0000000
#> NA12832 0.00000 0.0000000 0.0000000
#> NA11930 1.00000 1.0000000 1.0000000
#> NA12890 0.00000 0.0000000 0.6956522
#> NA07037 1.00000 1.0000000 1.0000000
#> NA07347 2.00000 2.0000000 1.0000000
#> NA12829 1.00000 1.0000000 1.0000000
#> NA12749 0.00000 0.0000000 2.0000000
#> NA11894 2.00000 2.0000000 1.0000000
#> NA12286 0.00000 0.0000000 0.0000000
#> NA10865 1.00000 1.0000000 0.6956522
#> NA10864 0.54375 2.0000000 1.0000000
#> NA10853 1.00000 1.0000000 1.0000000
#> NA11918 0.00000 0.0000000 0.0000000
#> NA12830 0.00000 0.0000000 0.0000000
#> NA12818 0.00000 0.0000000 0.0000000
#> NA10836 0.54375 2.0000000 1.0000000
#> NA11893 1.00000 1.0000000 0.0000000
#> NA11919 1.00000 1.0000000 2.0000000
#> NA12489 2.00000 2.0000000 2.0000000
#> NA12399 0.00000 0.0000000 0.0000000
#> NA12413 1.00000 1.0000000 1.0000000
#> NA10843 0.00000 0.0000000 1.0000000
#> NA12842 1.00000 1.0000000 1.0000000
#> NA12347 0.00000 0.0000000 0.0000000
#> NA07346 1.00000 1.0000000 1.0000000
#> NA12775 0.00000 0.0000000 1.0000000
#> NA07014 0.00000 0.0000000 1.0000000
#> NA12767 0.00000 0.0000000 1.0000000
#> NA12889 0.00000 0.0000000 1.0000000
#> NA12386 0.00000 0.0000000 0.0000000
#> NA06995 2.00000 2.0000000 2.0000000
#> NA12376 1.00000 1.0000000 1.0000000
#> NA12342 0.00000 0.0000000 0.0000000
#> NA12748 0.00000 0.0000000 0.0000000
#> NA11931 0.00000 0.0000000 1.0000000
#> NA12045 0.00000 0.0000000 1.0000000
#> NA12750 1.00000 1.0000000 1.0000000
#> NA11831 0.00000 0.0000000 0.0000000
#> NA12146 1.00000 1.0000000 0.0000000
#> NA11882 0.00000 0.0000000 1.0000000
#> NA07056 0.00000 0.0000000 1.0000000
#> NA12707 1.00000 1.0000000 0.6956522
#> NA12154 1.00000 1.0000000 1.0000000
#> NA12753 0.00000 0.0000000 0.0000000
#> NA11839 1.00000 1.0000000 1.0000000
#> NA10859 0.00000 0.0000000 1.0000000
#> NA12875 0.00000 0.0000000 0.0000000
#> NA07348 1.00000 1.0000000 1.0000000
#> NA12156 0.00000 0.0000000 0.0000000
#> NA12044 0.00000 0.0000000 0.0000000
#> NA11992 1.00000 1.0000000 0.0000000
#> NA11829 1.00000 1.0000000 1.0000000
#> NA12239 1.00000 1.0000000 1.0000000
#> NA12762 0.00000 0.0000000 0.0000000
#> NA12716 2.00000 2.0000000 2.0000000
#> NA12878 2.00000 2.0000000 2.0000000
#> NA10856 1.00000 1.0000000 1.0000000
#> NA12874 0.00000 0.0000000 1.0000000
#> NA12760 2.00000 2.0000000 0.0000000
#> NA06985 0.00000 0.0000000 0.0000000
#> NA12003 1.00000 1.0000000 0.0000000
#> NA10835 0.00000 0.0000000 0.0000000
#> NA07022 1.00000 1.0000000 0.0000000
#> NA12813 0.00000 0.0000000 0.6956522
#> NA10839 0.00000 0.0000000 1.0000000
#> NA07055 1.00000 1.0000000 1.0000000
#> NA12056 1.00000 1.0000000 1.0000000
#> NA10863 0.00000 0.0000000 0.0000000
#> NA12145 0.54375 2.0000000 1.0000000
#> NA12814 0.00000 0.0000000 0.0000000
#> NA10847 0.00000 0.5925926 0.0000000
#> NA12006 0.00000 0.0000000 0.0000000
#> NA12763 0.00000 0.0000000 1.0000000
#> NA07357 1.00000 1.0000000 1.0000000
#> NA12144 0.54375 2.0000000 1.0000000
#> NA10831 0.00000 0.0000000 0.0000000
#> NA07000 0.00000 0.0000000 0.0000000
#> NA11832 1.00000 1.0000000 0.0000000
#> NA06991 0.00000 0.0000000 1.0000000
#> NA11840 1.00000 1.0000000 0.0000000
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#> NA12376 0 0 0
#> NA12342 0 0 0
#> NA12748 0 0 0
#> NA11931 0 0 0
#> NA12045 0 0 0
#> NA12750 0 0 0
#> NA11831 1 1 1
#> NA12146 0 0 1
#> NA11882 0 0 1
#> NA07056 0 0 0
#> NA12707 0 0 0
#> NA12154 0 0 0
#> NA12753 0 0 0
#> NA11839 0 0 0
#> NA10859 0 0 1
#> NA12875 0 0 1
#> NA07348 0 0 1
#> NA12156 0 0 1
#> NA12044 0 0 0
#> NA11992 0 0 0
#> NA11829 0 0 0
#> NA12239 0 0 0
#> NA12762 0 0 0
#> NA12716 0 0 0
#> NA12878 0 0 0
#> NA10856 0 0 0
#> NA12874 0 0 0
#> NA12760 0 0 0
#> NA06985 0 0 0
#> NA12003 0 0 1
#> NA10835 1 1 1
#> NA07022 0 0 0
#> NA12813 0 0 0
#> NA10839 0 0 0
#> NA07055 0 0 0
#> NA12056 0 0 1
#> NA10863 1 1 1
#> NA12145 0 0 0
#> NA12814 0 0 0
#> NA10847 0 0 1
#> NA12006 0 0 0
#> NA12763 0 0 0
#> NA07357 0 0 0
#> NA12144 0 0 0
#> NA10831 0 0 0
#> NA07000 2 2 2
#> NA11832 0 0 2
#> NA06991 0 0 0
#> NA11840 1 1 1
#> NA12802 0 0 1
#> NA12761 0 0 1
#> NA10830 0 0 0
#> NA10855 1 1 2
#> NA06994 0 0 1
#> NA11993 1 1 1
#> NA11995 1 1 1
#> NA12891 0 0 0
#> NA12864 0 0 0
#> NA12751 0 0 1
#> NA10861 1 1 1
#> NA12005 0 0 0
#> NA12234 1 1 1
#> NA07345 0 0 1
#> NA07029 1 1 1
#> NA12892 0 0 0
#> NA12248 1 1 1
#> NA10846 0 0 0
#> NA12801 1 1 1
#> NA12872 0 0 0
#> NA12155 0 0 0
#> NA06993 0 0 0
#> NA11830 0 0 0
#> NA10838 0 0 1
#> NA12249 0 0 0
#> NA12057 0 0 0
#> NA12812 1 1 1
#> NA11881 0 0 0
#> NA11994 0 0 0
#> NA12873 0 0 0
#> NA12815 0 0 1
#> NA12740 0 0 1
#> NA12752 0 0 1
#> NA12043 0 0 0
#> NA12264 0 0 1
#> NA10854 1 1 1
#> NA12865 0 0 0
#> chr22:15460378:G:A chr22:15464609:G:A chr22:15467656:A:C
#> NA06989 0.0000000 0 0.0000000
#> NA11891 1.0000000 1 1.0000000
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#> NA12877 0.0000000 1 1.0000000
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#> NA12777 0.0000000 1 1.0000000
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#> NA12340 1.0000000 1 1.0000000
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#> NA11892 0.0000000 0 0.0000000
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#> NA10840 0.0000000 2 2.0000000
#> NA06997 0.0000000 1 1.0000000
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#> NA12718 1.0000000 1 1.0000000
#> NA12282 0.0000000 1 1.0000000
#> NA11920 0.0000000 0 0.0000000
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#> NA12336 1.0000000 1 1.0000000
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#> NA11894 2.0000000 2 2.0000000
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#> NA10865 0.0000000 0 0.0000000
#> NA10864 1.0000000 1 1.0000000
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#> NA10836 0.0000000 1 1.0000000
#> NA11893 1.0000000 1 1.0000000
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#> NA12489 0.0000000 0 0.0000000
#> NA12399 2.0000000 2 2.0000000
#> NA12413 1.0000000 2 2.0000000
#> NA10843 0.0000000 1 1.0000000
#> NA12842 0.0000000 1 1.0000000
#> NA12347 0.0000000 0 0.0000000
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#> NA10859 0.0000000 0 0.0000000
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#> NA12156 0.0000000 1 1.0000000
#> NA12044 0.0000000 0 0.0000000
#> NA11992 0.0000000 0 0.0000000
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#> NA12003 0.0000000 1 1.0000000
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#> NA12813 0.0000000 0 0.0000000
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#> NA10863 1.0000000 1 1.0000000
#> NA12145 0.0000000 0 0.0000000
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#> NA12801 1.0000000 1 1.0000000
#> NA12872 0.0000000 2 2.0000000
#> NA12155 1.0000000 1 1.0000000
#> NA06993 0.0000000 0 0.0000000
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#> chr22:15474749:C:A chr22:15476864:T:C chr22:15480497:C:T
#> NA06989 1 0 0.0000000
#> NA11891 0 2 0.0000000
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#> NA12341 0 1 1.0000000
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#> NA12275 1 1 1.0000000
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#> NA12383 0 1 1.0000000
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#> NA11892 0 0 0.0000000
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#> NA10840 0 1 1.0000000
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#> NA12282 0 1 1.0000000
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#> NA12829 0 0 0.0000000
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#> chr22:15483717:T:G chr22:15492342:C:T chr22:15496398:T:G
#> NA06989 0 0.0000000 1.0000000
#> NA11891 2 0.0000000 0.0000000
#> NA11843 0 0.0000000 0.0000000
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#> NA11892 0 0.0000000 0.0000000
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#> chr22:15498747:C:T chr22:15509738:T:C chr22:15512490:A:G
#> NA06989 0.000000 1.000000 1.0000000
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#> NA12383 1.000000 0.621118 0.0000000
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#> NA11892 0.000000 2.000000 0.0000000
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#> NA12843 1.000000 0.000000 1.0000000
#> NA12766 2.000000 0.000000 0.0000000
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#> NA06997 1.000000 1.000000 0.0000000
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