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

Paolo Momigliano paolo.momigliano at gmail.com
Fri Aug 7 09:29:26 CEST 2015


Hi Zhian,

thank you so much this worked perfectly.

Cheers

Paolo






On Fri, Aug 7, 2015 at 1:52 AM, Zhian Kamvar <
kamvarz at science.oregonstate.edu> wrote:

> This is due to an issue in pegas where it expects the alleles to be in
> numerical order for micro satellites.
>
> Until it's fixed, I have made a workaround here:
> https://gist.github.com/zkamvar/95af8adaf1b3f01a4995
>
> Copy + paste the function into your R console and then use
> resort_microsat(myData) for the workaround.
>
> Cheers,
> Zhian
>
> > On Aug 6, 2015, at 03:00 ,
> adegenet-forum-request at lists.r-forge.r-project.org wrote:
> >
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> >   1. Re: [adegenet forum] hw.test on genind object (Vojt?ch Zeisek)
> >
> >
> > ----------------------------------------------------------------------
> >
> > Message: 1
> > Date: Thu, 06 Aug 2015 09:42:39 +0200
> > From: Vojt?ch Zeisek <vojta at trapa.cz>
> > To: adegenet-forum at lists.r-forge.r-project.org
> > Subject: Re: [adegenet-forum] [adegenet forum] hw.test on genind
> >       object
> > Message-ID: <7057116.uogps0hNZK at veles>
> > Content-Type: text/plain; charset="utf-8"
> >
> > Dne ?t 6. srpna 2015 17:31:20, Paolo Momigliano napsal(a):
> >> Thanks for the tip,
> >>
> >> unfortunately using the genind2loci function to convert does not help (i
> >> guess that does the same as as.loci?). i used the HWE.test function in
> >
> > What was the error message? Hm, then the only idea (going back to Your
> error
> > messages) is this: Are You really absolutely sure You have all vectors
> of same
> > lengths? I mean specifically individual names, populations and all loci.
> How
> > do You mark missing data? Are there individual/population/loci names?
> How do
> > they look like? Does print(neu) say what You expect (number of loci and
> > individuals)? And what about summary(neu) - missing data and other
> > characteristics? Does print(neu, details=TRUE) look OK?
> >
> >> adegenet too before, yet i understand that this function is not present
> >> anymore in the new adegenet and its functionality is supposed to be
> >> replaced by pegas hwe.test?
> >>
> >> If i try to run HWE.est from adegenet i get this
> >>
> >>> HWE.test(neu)
> >>
> >> Error: could not find function "HWE.test"
> >>
> >> or
> >>
> >>> HWE.test.genind(neu)
> >>
> >> As of adegenet_1.5-0, this function has been removed and is replaced by
> >> 'hw.test' in the package 'pegas'
> >
> > Yes, I see. I haven't used newest adegenet much yet, so I missed that.
> >
> >> Did anyone have the same problem?
> >
> > Once I had problem with this function (I don't remember the error
> message)
> > when I had too much missing data (~15% in some loci). After removal of
> those
> > loci/individuals, it worked fine. But I guess this is not Your case
> now...
> >
> >> Cheers
> >>
> >> Paolo
> >
> > Good luck,
> > Vojt?ch
> >
> >> On Thu, Aug 6, 2015 at 5:18 PM, Vojt?ch Zeisek <vojta at trapa.cz> wrote:
> >>> Hi
> >>>
> >>> Dne ?t 6. srpna 2015 17:00:53, Paolo Momigliano napsal(a):
> >>>> 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)
> >>>
> >>> I use to use this function only with loci object (I use to start with
> >>> pegas'
> >>> read.loci function to import data), although man page says it should
> work
> >>> also
> >>> with genind. Might be You could try to convert Your genind object into
> >>> loci by
> >>> genind2loci function.
> >>>
> >>>> # 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?
> >>>
> >>> Adegenet also has function HWE.test.genind. It works fine for me on
> genind
> >>> objects.
> >>> There is also function HWE.test in package genetics, but I haven't
> used it
> >>> myself.
> >>>
> >>>> Thanks so much!
> >>>>
> >>>> Paolo
> >>>
> >>> HTH,
> >>> Vojt?ch
> > --
> > Vojt?ch Zeisek
> > http://trapa.cz/en/
> >
> > Department of Botany, Faculty of Science
> > Charles University in Prague
> > Ben?tsk? 2, Prague, 12801, CZ
> > http://botany.natur.cuni.cz/en/
> >
> > Institute of Botany, Academy of Science
> > Z?mek 1, Pr?honice, 25243, CZ
> > http://www.ibot.cas.cz/en/
> >
> > Czech Republic
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