search

EricArcher / strataG

strataG is a toolkit for haploid sequence and multilocus genetic data summaries, and analyses of population structure.
25 stars 12 forks source link

ldNe issues #21

Closed PatWright closed 4 years ago

PatWright commented 6 years ago

Hello,

I'm trying to calculate the ldNe for my data. For this, I first converted my genind file to gtype (genind2gtypes). The ldNe function, however, does not work after this is done. I get the warning message "No loci are biallelic", but the summary seems to show that my file is fine.

Thanks for your help!

> ldNe(gen50,maf.threshold = 0.02,ci=0.95)
NULL
Warning message:
No loci are biallelic. NULL returned. 
> summary(gen50)

<<< gtypes created on 2018-08-07 16:05:22 >>>

Contents: 680 samples, 14 loci, 2 strata

Strata summary:
            num.samples num.missing num.alleles prop.unique.alleles heterozygosity
SubPop0-130         130  0.07142857    10.64286          0.06907160      0.7647841
SubPop1-550         550  0.07142857    12.28571          0.01938025      0.7829731

Locus summary:
         num.genotyped num.alleles prop.unique.alleles obsvd.heterozygosity
A24                680          11          0.00000000            0.7323529
B22                680           8          0.00000000            0.7117647
CloneA2            680          12          0.08333333            0.7779412
Kpa24_2            680          17          0.00000000            0.9014706
Mluc8              680          10          0.00000000            0.8132353
Kpa16_2            680          14          0.00000000            0.8794118
CA38               678          16          0.00000000            0.8952802
CA11               680          12          0.00000000            0.6897059
Mnatt6             680          10          0.10000000            0.7808824
G6                 680           5          0.00000000            0.6705882
C112_2             680          11          0.00000000            0.6397059
MS3D02             680          17          0.05882353            0.6941176
H23_Mluc           680          15          0.06666667            0.8500000
B23                680          15          0.00000000            0.8764706
EricArcher commented 6 years ago

The ldNe function requires biallelic loci (SNPs). You'll notice in the summary of your data that the number alleles at each locus (num.alleles) is greater than two.