[adegenet-forum] [adegenet forum] hw.test on genind object

[Paolo Momigliano]

Hi all,

i am having some real trouble with a very simple task: running hw.test from
pegas which is supposed to work with adegenet.

i tried importing my files both from genepop and fstat using the
read.genepop and read.fstat functions:

below an example code

# load libraries
library(adegenet)
library(pegas)

# import data
neu<-read.genepop("snp1.gen", ncode = 3L)

# Calculate HWE for first pop
HWE_Ning<-hw.test(neu[1:23,], B=100)


at which point, i get warnings:

>There were 50 or more warnings (use warnings() to see the first 50)
> warnings()
Warning messages:
1: In O - E : longer object length is not a multiple of shorter object
length
2: In (O - E)^2/E :
  longer object length is not a multiple of shorter object length
3: In O - E : longer object length is not a multiple of shorter object
length
4: In (O - E)^2/E :
  longer object length is not a multiple of shorter object length
5: In O - E : longer object length is not a multiple of shorter object
length
6: In (O - E)^2/E :
  longer object length is not a multiple of shorter object length
7: In O - E : longer object length is not a multiple of shorter object
length

etc....

The hw.test function works just fine on the "nancycat" dataset from
Adegenet . But it doesn't whenever i import a dataset. I know the datasets
are not corrupted, as i have carried out a lot of other analyses in
adegenet and  diveRsity and never had a problem...

This problem persists if i try to convert the genind object using the
as.loci function before running hw.test.

Do you have any suggestion?


Thanks so much!

Paolo
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