GenABEL: meaning of numeric genotype values?
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Entering edit mode
8.2 years ago
biocyberman ▴ 870

I am trying to understand the numeric ouput of the conversion from character to numeric like below:

require(GenABEL)
data(srdta)
subdat <- srdta@gtdata[1:5,1:10]
as.genotype(subdat)
as.numeric(subdat)

My output:

> subdat <- srdta@gtdata[1:5,1:10]
> as.genotype(subdat)
   rs10 rs18 rs29 rs65 rs73 rs114 rs128 rs130 rs143 rs150
p1  T/T  G/G  G/G  T/A  A/A   A/A   G/G   A/A   G/G   A/A
p2  T/T  G/G <NA> <NA>  A/A   A/A   G/G   G/G   T/T   C/C
p3  T/T  G/G <NA>  T/A  A/A   A/A   G/G   A/A   G/G   A/A
p4  T/T  G/G <NA> <NA>  A/A   A/A   G/G   G/G  <NA>   A/C
p5  T/T  G/A  G/G  T/T  A/A   A/A   G/G   G/G   G/G   A/A
> as.numeric(subdat)
   rs10 rs18 rs29 rs65 rs73 rs114 rs128 rs130 rs143 rs150
p1    0    0    0    1    0     0     0     0     2     2
p2    0    0   NA   NA    0     0     0     2     0     0
p3    0    0   NA    1    0     0     0     0     2     2
p4    0    0   NA   NA    0     0     0     2    NA     1
p5    0    1    0    2    0     0     0     2     2     2

What do 0, 1, 2, and NA mean?

R genabel gwas • 1.7k views
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