Erroneous imputation result #56
Description
I used rsXXX, 999999, 111111 to censor the data that I'm looking at. I checked three positions. chr1.dose is the imputed dataset. FFFFFF is the original dataset.
What I have found problematic is that the imputation completely changed the information on the original dataset. As opposed to simply filling in missing values, the reference / alternative alleles have been changed. There isn't a consistent pattern (e.g. it's not a simple matter of flipping strands) and I don't know what's happening in between.
> chr1.dose$map$allele1[chr1.dose$map$physical.pos==111111]
[1] "T"
> chr1.dose$map$allele2[chr1.dose$map$physical.pos==111111]
[1] "G"
> chr1.dose$genotypes[,chr1.dose$map$physical.pos== 111111]
[1] 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
[59] 2 2 2 2 2 2 2 2 2 2 2 2 0 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 0 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 1 2 2 2 2 2 2 2 2
[117] 2 1 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 0 2 2 2 2 2 2 2 2 2 2 2 2 2
[175] 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 0 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
[233] 2 2 2 1 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
[291] 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
[349] 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
[407] 2 2 2 1 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
[465] 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
[523] 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 1 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
[581] 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 1 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
>
> FFFFFF$map$allele1[FFFFFF$map$marker.ID=="rsXXX"]
[1] "A"
> FFFFFF$map$allele2[FFFFFF$map$marker.ID=="rsXXX"]
[1] "C"
> FFFFFF$genotypes[,FFFFFF$map$marker.ID=="rsXXX"]
[1] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
[59] 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0
[117] 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0
[175] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
[233] 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
[291] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
[349] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
[407] 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
[465] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
[523] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
[581] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
> FFFFFF$map$physical.pos[FFFFFF$map$marker.ID=="rsXXX"]
[1] 999999
>
> chr1.dose$map$allele1[chr1.dose$map$physical.pos==222222]
[1] "T"
> chr1.dose$map$allele2[chr1.dose$map$physical.pos== 222222]
[1] "C"
> chr1.dose$genotypes[,chr1.dose$map$physical.pos== 222222]
[1] 0 1 2 2 1 1 2 2 0 2 2 2 2 2 2 1 2 2 2 2 2 1 2 2 2 2 2 2 2 0 2 2 0 2 2 2 2 2 2 2 2 1 0 2 2 2 2 2 2 1 2 2 2 2 2 2 2 2
[59] 2 2 2 2 2 2 1 1 2 2 2 2 2 0 2 1 2 2 2 2 1 1 2 0 2 2 2 0 2 2 2 2 1 2 2 2 2 0 2 2 1 2 2 2 2 1 1 2 2 2 0 0 2 1 2 2 2 2
[117] 2 2 2 2 0 2 1 2 0 2 2 2 2 2 0 2 2 2 2 2 2 2 2 0 2 2 0 0 0 2 1 2 2 1 2 0 2 2 1 2 2 2 2 2 2 2 0 2 2 2 1 2 2 2 2 2 1 1
[175] 2 1 2 2 0 1 1 2 2 2 0 0 2 2 2 0 0 2 2 2 2 2 2 2 2 2 2 2 2 0 2 2 2 2 1 2 2 0 2 2 2 2 0 0 2 2 2 2 1 2 1 2 2 2 2 2 2 0
[233] 2 2 2 2 2 2 2 0 2 2 2 2 1 2 2 0 0 2 2 2 2 2 1 2 0 2 2 2 0 2 1 2 0 2 0 2 2 2 0 2 2 2 2 2 0 2 0 2 2 0 1 2 2 2 2 2 2 2
[291] 0 2 2 1 2 2 2 2 2 1 1 2 2 2 2 2 2 2 2 2 1 2 2 2 2 2 2 1 2 2 2 2 2 2 2 2 2 2 0 2 2 2 2 2 2 2 0 2 2 0 2 2 2 2 1 1 2 0
[349] 2 0 2 0 2 2 2 1 2 0 1 2 0 2 2 2 1 0 1 2 2 2 2 2 0 2 2 2 0 0 0 2 2 2 2 1 0 0 1 1 2 2 2 2 1 2 2 1 2 1 2 2 2 0 2 1 2 2
[407] 1 2 2 2 1 2 1 2 2 2 2 2 2 2 2 1 1 2 2 2 0 0 0 2 2 0 0 2 2 2 2 1 2 2 2 1 2 2 2 1 2 1 2 0 1 0 2 2 1 2 1 0 2 0 2 2 1 2
[465] 2 2 2 2 0 2 2 2 2 2 2 1 2 2 2 2 1 2 2 2 2 0 1 2 2 0 2 0 2 2 2 2 0 2 2 0 2 1 0 0 2 0 2 2 2 2 2 2 2 2 0 0 2 2 1 1 0 2
[523] 1 2 2 0 2 2 2 2 2 2 2 1 2 2 2 2 1 2 2 2 2 2 2 2 0 2 1 2 2 2 2 1 0 1 1 2 2 2 2 2 1 0 2 2 0 2 2 1 2 0 2 2 2 0 0 2 2 2
[581] 2 1 2 2 2 2 2 2 2 2 0 2 1 2 2 0 2 1 2 2 2 2 2 2 2 1 2 1 2 2 1 0 2 2 2 2 0 2 0 2 2 2 2 2 2 2 2 2 2 2 1 2
>
> FFFFFF$map$allele1[FFFFFF$map$marker.ID=="rsYYY"]
[1] "A"
> FFFFFF$map$allele2[FFFFFF$map$marker.ID=="rsYYY"]
[1] "G"
> FFFFFF$genotypes[,FFFFFF$map$marker.ID=="rsYYY"]
[1] 1 1 0 0 1 1 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 2 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0
[59] 0 0 0 0 0 0 1 1 0 0 0 0 0 1 0 1 0 0 0 0 1 1 0 1 0 0 0 1 0 0 0 0 1 0 0 0 0 1 0 0 1 0 0 0 0 1 1 0 0 0 1 2 0 1 0 0 0 0
[117] 0 0 0 0 1 0 1 0 1 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 1 1 1 0 1 0 0 1 0 2 0 0 1 0 0 0 0 0 0 0 1 0 0 0 1 0 0 0 0 0 1 1
[175] 0 1 0 0 1 1 1 0 0 0 1 1 0 0 0 2 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 1 0 0 1 0 0 0 0 2 1 0 0 0 0 1 0 1 0 0 0 0 0 0 1
[233] 0 0 0 0 0 0 0 1 0 0 0 0 1 0 0 1 1 0 0 0 0 0 1 0 1 0 0 0 2 0 1 0 1 0 1 0 0 0 1 0 0 0 0 0 1 0 1 0 0 1 1 0 0 0 0 0 0 0
[291] 1 0 0 1 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 2 0 0 1 0 0 0 0 1 1 0 1
[349] 0 1 0 1 0 0 0 1 0 1 1 0 1 0 0 0 1 1 1 0 0 0 0 0 1 0 0 0 2 1 1 0 0 0 0 1 1 1 1 1 0 0 0 0 1 0 0 1 0 1 0 0 0 1 0 1 0 0
[407] 1 0 0 0 1 0 1 0 0 0 0 0 0 0 0 1 1 0 0 0 1 1 1 0 0 1 1 0 0 0 0 1 0 0 0 1 0 0 0 1 0 1 0 1 1 1 0 0 1 0 1 2 0 1 0 0 1 0
[465] 0 0 0 0 2 0 0 0 0 0 0 1 0 0 0 0 1 0 0 0 0 1 1 0 0 1 0 1 0 0 0 0 1 0 0 2 0 1 2 2 0 1 0 0 0 0 0 0 0 0 1 2 0 0 1 1 2 0
[523] 1 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 1 0 0 0 0 0 0 0 1 0 1 0 0 0 0 1 2 1 1 0 0 0 0 0 1 1 0 0 1 0 0 1 0 1 0 0 0 1 1 0 0 0
[581] 0 1 0 0 0 0 0 0 0 0 2 0 1 0 0 1 0 1 0 0 0 0 0 0 0 1 0 1 0 0 1 1 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0
> FFFFFF$map$physical.pos[FFFFFF$map$marker.ID=="rsYYY"]
[1] 888888
>
> chr1.dose$map$allele1[chr1.dose$map$physical.pos==333333]
[1] "A"
> chr1.dose$map$allele2[chr1.dose$map$physical.pos== 333333]
[1] "G"
> chr1.dose$genotypes[,chr1.dose$map$physical.pos== 333333]
[1] 0 0 0 0 0 0 0 1 0 1 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 2 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1
[59] 1 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 1 2 0 0 0 0 0 0 0 2 0 0 0
[117] 1 2 0 0 1 2 1 0 0 2 0 0 0 0 1 0 0 1 1 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0
[175] 0 0 0 0 0 0 1 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 2 0 0 0 1 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0
[233] 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0
[291] 2 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 2 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 1 0 0 1 0 0 0 0 0 0 0 0
[349] 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 2 0 1 1 0 0 0 0 0 0 0 1 0 0 0 0 0 2 0 0 0 1 0 1 1 0 0 0 1 0
[407] 0 0 0 0 2 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 1 0 1 2 0 0 2 0 0 0 1 0 0
[465] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 1 0 0 0 0 1 0 0 0 0 1 0 0 2 0 0 0 1 0 0 0 0 0 0 0 0 0 2 0 0 2 0 0 0 0 1 0
[523] 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 0 1 0 2 1 0 0 0 0 0 1 0 0 0 0 0 0 0 2 0 0 0 0 0 2 2 0 0 0 0 1 0 0 0 0 0 0 1
[581] 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
>
> FFFFFF$map$allele1[FFFFFF$map$marker.ID=="rsZZZ"]
[1] "G"
> FFFFFF$map$allele2[FFFFFF$map$marker.ID=="rsZZZ"]
[1] "A"
> FFFFFF$genotypes[,FFFFFF$map$marker.ID=="rsZZZ"]
[1] 0 1 0 0 0 0 0 1 0 1 0 0 1 0 0 1 0 0 0 1 0 0 1 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 1
[40] 2 0 0 1 1 0 0 0 0 0 1 1 0 0 0 0 0 1 1 1 0 0 0 0 NA 1 0 0 0 1 0 1 1 1 1 0 1 0 1
[79] 0 1 0 1 0 0 1 0 0 1 0 0 0 0 1 0 1 0 0 0 0 NA 0 0 0 1 2 0 0 1 0 0 0 1 2 0 0 0 1
[118] 2 0 0 1 2 1 0 0 2 1 0 0 0 1 0 1 1 1 0 0 1 0 0 0 0 0 1 1 0 1 0 0 0 0 0 1 0 0 0
[157] 0 0 0 1 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 1 1 0 1 1 0 0 0 0 0 0 1 0 1 1 0
[196] 0 0 0 0 0 0 0 0 0 0 0 1 2 0 0 0 1 0 1 0 1 1 0 0 0 1 1 1 0 0 0 0 0 0 1 0 0 0 1
[235] 1 1 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 1 0 0 0 1 0 0 1 0 0 0 0 1 0 0 0 0 0 0 0 1
[274] 0 0 0 0 1 0 1 0 0 0 0 0 0 1 0 0 NA 2 0 1 0 NA 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0
[313] 2 0 0 1 0 1 1 0 0 1 0 0 1 0 0 0 0 0 0 1 1 0 0 0 1 0 0 1 0 0 0 0 1 1 0 0 1 0 0
[352] 0 0 0 2 0 0 0 0 0 0 0 0 1 1 1 0 0 0 1 0 1 1 0 0 0 2 0 1 1 0 1 0 0 0 0 0 1 1 0
[391] 0 0 0 2 0 0 0 1 0 1 1 0 1 0 1 0 0 0 0 0 2 0 1 0 0 1 1 0 0 0 0 0 1 0 0 0 0 0 1
[430] 1 1 0 0 0 0 0 0 1 0 0 0 1 0 0 1 1 1 1 0 0 0 1 0 1 2 0 1 2 0 1 0 1 0 1 1 0 1 0
[469] 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 1 0 0 0 0 1 1 0 0 0 1 0 1 2 0 0 0 1 0 0 0 0
[508] 1 1 0 0 0 2 0 0 2 1 0 1 0 1 0 1 1 0 0 0 0 0 0 0 0 0 0 1 1 0 0 1 0 0 0 0 1 0 2
[547] 1 0 1 1 0 1 1 0 0 0 0 0 0 0 2 0 0 0 0 0 2 2 0 0 0 0 1 0 1 0 0 0 0 1 0 1 0 1 0
[586] 1 1 0 0 1 1 0 0 1 0 0 0 1 0 0 1 1 1 1 0 1 0 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0
[625] 0 0 0 1 1 1 0 0
> FFFFFF$map$physical.pos[FFFFFF$map$marker.ID=="rsZZZ"]
[1] 777777