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?