**340**wrote:

I am trying to generate an LD plot using LDheatmap in R.

I have 4 SNPs geotyped for around 80 000 individuals :

```
head(m.genos)
p1205 p0864 p3077 p1244
1 G/G C/C T/T C/C
2 A/A C/C T/T C/C
3 G/G T/T T/T T/T
4 A/A C/C T/T C/C
5 G/G C/C T/T C/C
6 G/A C/C T/T C/C
MyHeatmap <- LDheatmap(m.genos, genetic.distances = as.numeric(m.dist),distances="physical",LDmeasure="r",title="LD analysis",
add.map=TRUE,add.key=TRUE,flip=TRUE,SNP.name=names[1:4])
```

However, the LDheatmap function computes the ld matrix using ONLY 3 of them.

```
> MyHeatmap$LDmatrix
p3077 p1205 p0864
p3077 NA 0.02379055 0.02184959
p1205 NA NA 0.21808013
p0864 NA NA NA
```

I have managed to succesfully generate the LD matrix for other SNPs, so I was wondering what could me the problem in this case?

**The excluded SNP is tri allelic :** => possibly causing the LDheatmap function to fail in generating the complete LD matrix

```
Number of samples typed: 87058 (99.8%)
Allele Frequency: (3 alleles)
Count Proportion
C 110853 0.64
T 54539 0.31
A 8724 0.05
NA 272 NA
Genotype Frequency:
Count Proportion
C/C 35354 0.41
C/T 34647 0.40
C/A 5498 0.06
T/T 8552 0.10
T/A 2788 0.03
A/A 219 0.00
NA 136 NA
Heterozygosity (Hu) = 0.4940388
Poly. Inf. Content = 0.4119684
```

**2.3k**• written 6.2 years ago by Agatha •

**340**