[adegenet-forum] DAPC error

[Jombart, Thibaut]

Hello,

it looks like your object contains only one population:
> cnt75_cl94_all <- read.structure("Excelformat_cnt75_cl94_2-16_ml80_maf0.10_missing0.8_hwe0.05.stru", n.ind=98, n.loc=735, onerowperind=TRUE, col.lab=1, col.pop=2, row.marknames=1, NA.char="0")

 Which other optional columns should be read (press 'return' when done)? 1:

 Converting data from a STRUCTURE .stru file to a genind object...

> cnt75_cl94_all
/// GENIND OBJECT /////////

 // 98 individuals; 735 loci; 1,470 alleles; size: 932.8 Kb

 // Basic content
   @tab:  98 x 1470 matrix of allele counts
   @loc.n.all: number of alleles per locus (range: 2-2)
   @loc.fac: locus factor for the 1470 columns of @tab
   @all.names: list of allele names for each locus
   @ploidy: ploidy of each individual  (range: 2-2)
   @type:  codom
   @call: read.structure(file = "Excelformat_cnt75_cl94_2-16_ml80_maf0.10_missing0.8_hwe0.05.stru",
    n.ind = 98, n.loc = 735, onerowperind = TRUE, col.lab = 1,
    col.pop = 2, row.marknames = 1, NA.char = "0")

 // Optional content
   @pop: population of each individual (group size range: 98-98)
> pop(cnt75_cl94_all)
 1  2  3  4  5  6  7  8  9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52
 1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1
53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98
 1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1
Levels: 1

Cheers
Thibaut




________________________________
From: adegenet-forum-bounces at lists.r-forge.r-project.org [adegenet-forum-bounces at lists.r-forge.r-project.org] on behalf of LAURA NICOLE WOODINGS [17869067 at students.latrobe.edu.au]
Sent: 05 October 2015 04:43
To: adegenet-forum at lists.r-forge.r-project.org
Subject: [adegenet-forum] DAPC error

Hi,

I am using adegenet to perform a DAPC on some SNP data. When I run the DAPC using the following command:
Dapc_cnt75_cl94_all <- dapc(cnt75_cl94_all, grp=Cluster_cnt75_cl94_k15$grp
I get this error: Error in svd(X, nu = 0L) : infinite or missing values in ‘x’
I have checked that all the group memberships are in the input file using “pop(cnt75_cl94_all)” and all group memberships are present.
The code I use to read in the original structure input file is:
cnt75_cl94_all <- read.structure("../Excelformat_cnt75_cl94_2-16_ml80_maf0.10_missing0.8_hwe0.05.stru", n.ind=98, n.loc=735, onerowperind=TRUE, col.lab=1, col.pop=2, row.marknames=1, NA.char="0", missing=0)

I am not sure why I am getting this error. I have attached my input file. Any help would be much appreciated.

Thanks,
Laura

PhD Candidate
Department of Ecology, Environment and Evolution| La Trobe University | Bundoora 3086 | Australia

m: +61 408 642 006 | e: 17869067 at students.latrobe.edu.au
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