Question: LOD Score NaN Error
1
gravatar for Abdul Rafay Khan
16 months ago by
Karachi, PK
Abdul Rafay Khan1.1k wrote:
library(paramlink) 

y = read.table("markers.txt", header=TRUE) 
x = linkdat(y, model=1)

lod(x)

Result:

LOD:    NaN

Data:

FAMID   ID  FID MID SEX AFF M_A1 M_A2
1   1   0   0   1   1   2   3
1   2   0   0   2   1   1   2
1   3   1   2   2   2   2   2
1   4   1   2   1   2   2   3
1   5   1   2   2   1   1   2
1   6   1   2   2   1   1   2
1   7   1   2   2   1   1   2
1   8   1   2   1   1   1   2
R paramlink score lod • 298 views
ADD COMMENTlink modified 16 months ago by zx87549.6k • written 16 months ago by Abdul Rafay Khan1.1k
1

From the manual:

If a marker has incompatible values (i.e. if a child of homozygous 1/1 parents has a 2 allele), the corresponding output entries are NaN.

ADD REPLYlink written 16 months ago by zx87549.6k

but my data seems correct

ADD REPLYlink written 16 months ago by Abdul Rafay Khan1.1k
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