[adegenet-forum] find.clusters missing values

[Thibaut Jombart]

Hi Marta,

the function find.clusters has methods for matrix and data.frame objects.
Easiest way to proceed is use 'tab' to extract allele frequencies from your
genind object and replace missing values, and then use find.clusters on it.

For instance:

> data(microbov)
> summary(microbov)

// Number of individuals: 704
// Group sizes: 50 50 51 30 50 50 47 61 31 55 50 50 49 30 50
// Number of alleles per locus: 9 7 12 5 11 9 7 12 13 9 13 16 14 14 14 10
10 19 11 13 17 12 16 13 12 15 8 22 21 9
// Number of alleles per group: 251 235 143 179 194 212 146 196 176 200 213
186 191 168 188
*// Percentage of missing data: 2.32 %*
// Observed heterozygosity: 0.55 0.54 0.69 0.45 0.64 0.6 0.29 0.59 0.68
0.58 0.66 0.71 0.6 0.71 0.8 0.64 0.45 0.64 0.65 0.63 0.66 0.66 0.59 0.74
0.68 0.77 0.62 0.69 0.68 0.44
// Expected heterozygosity: 0.71 0.6 0.78 0.54 0.79 0.76 0.49 0.69 0.83
0.77 0.77 0.82 0.75 0.76 0.89 0.75 0.63 0.77 0.75 0.78 0.77 0.77 0.77 0.84
0.74 0.89 0.69 0.77 0.89 0.56

> x <- tab(microbov, freq=TRUE, *NA.method="mean"*) # replace missing
values here
> g <- find.clusters(x)
Choose the number PCs to retain (>=1):
....

Best
Thibaut


--
Dr Thibaut Jombart
Lecturer, Department of Infectious Disease Epidemiology
Imperial College London
https://sites.google.com/site/thibautjombart/
https://github.com/thibautjombart
Twitter: @TeebzR <https://twitter.com/TeebzR>

On 1 August 2016 at 14:18, Marta Piotrowska <Marta.Piotrowska at sruc.ac.uk>
wrote:

> Dear Members,
>
>
>
> I am trying to use find.cluster function in adegenet package for my
> microsat data analysis but I can’t find anywhere information if it accepts
> missing values. I tried NAs but it seems not to like it. I know that one
> way around it is to remove all the samples with missing values but I
> wondered if there is alternative allowing me to keep the missing values?
>
>
>
> I will be grateful for your help.
>
>
>
> Regards,
>
> Marta
>
>
>
>
>
> *Marta Piotrowska, PhD.*
>
> *Postdoctoral Researcher*
>
> *Crop and Soil Systems Group*
>
> *SRUC*
>
> *West Mains Road*
>
> *Edinburgh EH9 3JG*
>
>
>
> *Phone: 01315354294*
>
> *Marta.Piotrowska at sruc.ac.uk <Marta.Piotrowska at sruc.ac.uk>*
>
>
>
>
>
>
>
>
>
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