[adegenet-forum] adegenet-forum Digest, Vol 74, Issue 9
Spencer Bruce
goatsrunfaster at gmail.com
Fri Oct 24 16:29:58 CEST 2014
Hello All,
Thanks for the tip Francesco! This almost works for me...
when I enter the code below in an attempt to randomly sample 20 individuals
from the genind object "tdhybrids" I get back the new genind object called
Random, I then used genind2genotype to view the contents of "Random" but
there are only 2 individuals (not 20)? The code I used is below:
Random <- tdhybrids[sample(tdhybrids$tab, 20), ]
obj <- genind2genotype(Random)
Am I missing something here? A big thank you to everyone in advance for
putting up with my questions?
-Spencer
On Thu, Oct 23, 2014 at 11:19 AM, Francesco Montinaro <
francesco.montinaro at gmail.com> wrote:
> Hi,
> I think that the problem is that since a genind object is a list, the nrow
> is NULL.
>
> Probably you want to sample from object$tab instead.
>
> Hope it helps.
>
> Best
>
>
>
> Francesco Montinaro
>
> On 23 October 2014 16:04, <
> adegenet-forum-request at lists.r-forge.r-project.org> wrote:
>
>> Send adegenet-forum mailing list submissions to
>> adegenet-forum at lists.r-forge.r-project.org
>>
>> To subscribe or unsubscribe via the World Wide Web, visit
>>
>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/adegenet-forum
>>
>> or, via email, send a message with subject or body 'help' to
>> adegenet-forum-request at lists.r-forge.r-project.org
>>
>> You can reach the person managing the list at
>> adegenet-forum-owner at lists.r-forge.r-project.org
>>
>> When replying, please edit your Subject line so it is more specific
>> than "Re: Contents of adegenet-forum digest..."
>>
>>
>> Today's Topics:
>>
>> 1. repooling random rows from genind objects (Spencer Bruce)
>> 2. Re: repooling random rows from genind objects (Jombart, Thibaut)
>> 3. Re: repooling random rows from genind objects (Spencer Bruce)
>> 4. Re: repooling random rows from genind objects (Jombart, Thibaut)
>> 5. Re: repooling random rows from genind objects (Spencer Bruce)
>>
>>
>> ----------------------------------------------------------------------
>>
>> Message: 1
>> Date: Thu, 23 Oct 2014 10:29:10 -0400
>> From: Spencer Bruce <goatsrunfaster at gmail.com>
>> To: adegenet-forum at lists.r-forge.r-project.org
>> Subject: [adegenet-forum] repooling random rows from genind objects
>> Message-ID:
>> <CAGjKGeaQyQ=
>> UFFOSerHR1qeKXHSwVzF-0whQf2do83wOV38s5w at mail.gmail.com>
>> Content-Type: text/plain; charset="utf-8"
>>
>> Hello All!
>>
>> I have three seperate populations as genind objects. What I would like to
>> do is pull a certain number of random individuals from each, to form a new
>> single genind population.
>>
>> I would then like individuals from this new genind population to mate
>> randomly, producing another genind object which would contain their
>> offspring.
>>
>> Below is the code I came up with (which does not work):
>>
>> Year1 <- repool(F1[sample(nrow(F1), 500), ], pop1[sample(nrow(pop1), 750),
>> ], pop2[sample(nrow(pop2), 750), ], n=2000)
>>
>> Year2 <- hybridize(Year1[sample(nrow(Year1), 1000), ],
>> Year1[sample(nrow(Year1), 1000), ], n=2000)
>>
>>
>> any help would be greatly appreciated!
>>
>> Best,
>> Spencer
>>
>> --
>> Spencer A Bruce
>> 200 Washington St.
>> Troy, NY 12180
>> 518 225 0787
>> -------------- next part --------------
>> An HTML attachment was scrubbed...
>> URL: <
>> http://lists.r-forge.r-project.org/pipermail/adegenet-forum/attachments/20141023/cb94a767/attachment-0001.html
>> >
>>
>> ------------------------------
>>
>> Message: 2
>> Date: Thu, 23 Oct 2014 14:50:24 +0000
>> From: "Jombart, Thibaut" <t.jombart at imperial.ac.uk>
>> To: Spencer Bruce <goatsrunfaster at gmail.com>,
>> "adegenet-forum at lists.r-forge.r-project.org"
>> <adegenet-forum at lists.r-forge.r-project.org>
>> Subject: Re: [adegenet-forum] repooling random rows from genind
>> objects
>> Message-ID:
>> <2CB2DA8E426F3541AB1907F98ABA6570ABE6AE7F at icexch-m1.ic.ac.uk>
>> Content-Type: text/plain; charset="iso-8859-1"
>>
>>
>> Hello,
>> hard to figure out what is wrong without the error message..
>> 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 Spencer
>> Bruce [goatsrunfaster at gmail.com]
>> Sent: 23 October 2014 15:29
>> To: adegenet-forum at lists.r-forge.r-project.org
>> Subject: [adegenet-forum] repooling random rows from genind objects
>>
>> Hello All!
>>
>> I have three seperate populations as genind objects. What I would like to
>> do is pull a certain number of random individuals from each, to form a new
>> single genind population.
>>
>> I would then like individuals from this new genind population to mate
>> randomly, producing another genind object which would contain their
>> offspring.
>>
>> Below is the code I came up with (which does not work):
>>
>> Year1 <- repool(F1[sample(nrow(F1), 500), ], pop1[sample(nrow(pop1),
>> 750), ], pop2[sample(nrow(pop2), 750), ], n=2000)
>>
>> Year2 <- hybridize(Year1[sample(nrow(Year1), 1000), ],
>> Year1[sample(nrow(Year1), 1000), ], n=2000)
>>
>>
>> any help would be greatly appreciated!
>>
>> Best,
>> Spencer
>>
>> --
>> Spencer A Bruce
>> 200 Washington St.
>> Troy, NY 12180
>> 518 225 0787
>> -------------- next part --------------
>> An HTML attachment was scrubbed...
>> URL: <
>> http://lists.r-forge.r-project.org/pipermail/adegenet-forum/attachments/20141023/c43c29fe/attachment-0001.html
>> >
>>
>> ------------------------------
>>
>> Message: 3
>> Date: Thu, 23 Oct 2014 10:52:59 -0400
>> From: Spencer Bruce <goatsrunfaster at gmail.com>
>> To: "Jombart, Thibaut" <t.jombart at imperial.ac.uk>
>> Cc: "adegenet-forum at lists.r-forge.r-project.org"
>> <adegenet-forum at lists.r-forge.r-project.org>
>> Subject: Re: [adegenet-forum] repooling random rows from genind
>> objects
>> Message-ID:
>> <
>> CAGjKGeZhjLhurZbKiMZxSmZV_GFC3quw58FPt06LrXwakRDPeA at mail.gmail.com>
>> Content-Type: text/plain; charset="utf-8"
>>
>> Error message:
>>
>> Error in sample.int(length(x), size, replace, prob) :
>> invalid first argument
>>
>> On Thu, Oct 23, 2014 at 10:50 AM, Jombart, Thibaut <
>> t.jombart at imperial.ac.uk
>> > wrote:
>>
>> >
>> > Hello,
>> > hard to figure out what is wrong without the error message..
>> > 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
>> Spencer
>> > Bruce [goatsrunfaster at gmail.com]
>> > *Sent:* 23 October 2014 15:29
>> > *To:* adegenet-forum at lists.r-forge.r-project.org
>> > *Subject:* [adegenet-forum] repooling random rows from genind objects
>> >
>> > Hello All!
>> >
>> > I have three seperate populations as genind objects. What I would like
>> > to do is pull a certain number of random individuals from each, to form
>> a
>> > new single genind population.
>> >
>> > I would then like individuals from this new genind population to mate
>> > randomly, producing another genind object which would contain their
>> > offspring.
>> >
>> > Below is the code I came up with (which does not work):
>> >
>> > Year1 <- repool(F1[sample(nrow(F1), 500), ], pop1[sample(nrow(pop1),
>> > 750), ], pop2[sample(nrow(pop2), 750), ], n=2000)
>> >
>> > Year2 <- hybridize(Year1[sample(nrow(Year1), 1000), ],
>> > Year1[sample(nrow(Year1), 1000), ], n=2000)
>> >
>> >
>> > any help would be greatly appreciated!
>> >
>> > Best,
>> > Spencer
>> >
>> > --
>> > Spencer A Bruce
>> > 200 Washington St.
>> > Troy, NY 12180
>> > 518 225 0787
>> >
>>
>>
>>
>> --
>> Spencer A Bruce
>> 200 Washington St.
>> Troy, NY 12180
>> 518 225 0787
>> -------------- next part --------------
>> An HTML attachment was scrubbed...
>> URL: <
>> http://lists.r-forge.r-project.org/pipermail/adegenet-forum/attachments/20141023/19bc54c8/attachment-0001.html
>> >
>>
>> ------------------------------
>>
>> Message: 4
>> Date: Thu, 23 Oct 2014 14:54:53 +0000
>> From: "Jombart, Thibaut" <t.jombart at imperial.ac.uk>
>> To: Spencer Bruce <goatsrunfaster at gmail.com>
>> Cc: "adegenet-forum at lists.r-forge.r-project.org"
>> <adegenet-forum at lists.r-forge.r-project.org>
>> Subject: Re: [adegenet-forum] repooling random rows from genind
>> objects
>> Message-ID:
>> <2CB2DA8E426F3541AB1907F98ABA6570ABE6AE93 at icexch-m1.ic.ac.uk>
>> Content-Type: text/plain; charset="iso-8859-1"
>>
>>
>>
>> What does nrow(F1) and other nrow(...)'s say?
>>
>>
>>
>>
>> ________________________________
>> From: Spencer Bruce [goatsrunfaster at gmail.com]
>> Sent: 23 October 2014 15:52
>> To: Jombart, Thibaut
>> Cc: adegenet-forum at lists.r-forge.r-project.org
>> Subject: Re: [adegenet-forum] repooling random rows from genind objects
>>
>> Error message:
>>
>> Error in sample.int<http://sample.int>(length(x), size, replace, prob) :
>> invalid first argument
>>
>> On Thu, Oct 23, 2014 at 10:50 AM, Jombart, Thibaut <
>> t.jombart at imperial.ac.uk<mailto:t.jombart at imperial.ac.uk>> wrote:
>>
>> Hello,
>> hard to figure out what is wrong without the error message..
>> Cheers
>> Thibaut
>> ________________________________
>> From: adegenet-forum-bounces at lists.r-forge.r-project.org<mailto:
>> adegenet-forum-bounces at lists.r-forge.r-project.org> [
>> adegenet-forum-bounces at lists.r-forge.r-project.org<mailto:
>> adegenet-forum-bounces at lists.r-forge.r-project.org>] on behalf of
>> Spencer Bruce [goatsrunfaster at gmail.com<mailto:goatsrunfaster at gmail.com>]
>> Sent: 23 October 2014 15:29
>> To: adegenet-forum at lists.r-forge.r-project.org<mailto:
>> adegenet-forum at lists.r-forge.r-project.org>
>> Subject: [adegenet-forum] repooling random rows from genind objects
>>
>> Hello All!
>>
>> I have three seperate populations as genind objects. What I would like to
>> do is pull a certain number of random individuals from each, to form a new
>> single genind population.
>>
>> I would then like individuals from this new genind population to mate
>> randomly, producing another genind object which would contain their
>> offspring.
>>
>> Below is the code I came up with (which does not work):
>>
>> Year1 <- repool(F1[sample(nrow(F1), 500), ], pop1[sample(nrow(pop1),
>> 750), ], pop2[sample(nrow(pop2), 750), ], n=2000)
>>
>> Year2 <- hybridize(Year1[sample(nrow(Year1), 1000), ],
>> Year1[sample(nrow(Year1), 1000), ], n=2000)
>>
>>
>> any help would be greatly appreciated!
>>
>> Best,
>> Spencer
>>
>> --
>> Spencer A Bruce
>> 200 Washington St.
>> Troy, NY 12180
>> 518 225 0787<tel:518%20225%200787>
>>
>>
>>
>> --
>> Spencer A Bruce
>> 200 Washington St.
>> Troy, NY 12180
>> 518 225 0787
>> -------------- next part --------------
>> An HTML attachment was scrubbed...
>> URL: <
>> http://lists.r-forge.r-project.org/pipermail/adegenet-forum/attachments/20141023/2dfd9408/attachment-0001.html
>> >
>>
>> ------------------------------
>>
>> Message: 5
>> Date: Thu, 23 Oct 2014 11:03:54 -0400
>> From: Spencer Bruce <goatsrunfaster at gmail.com>
>> To: "Jombart, Thibaut" <t.jombart at imperial.ac.uk>
>> Cc: "adegenet-forum at lists.r-forge.r-project.org"
>> <adegenet-forum at lists.r-forge.r-project.org>
>> Subject: Re: [adegenet-forum] repooling random rows from genind
>> objects
>> Message-ID:
>> <
>> CAGjKGeZiyS-27oF2CKb6JBPgS+VSyTA1-NS2Q8g2UC0JqOs4VA at mail.gmail.com>
>> Content-Type: text/plain; charset="utf-8"
>>
>> they both say Null, if I just type them into R.
>>
>> Just to be clear these genind objects contains microsat data for 11 loci
>> for thousands of individuals.
>>
>> I'm rather new to R, so I apologize if I'm missing something obvious
>> here...
>>
>> On Thu, Oct 23, 2014 at 10:54 AM, Jombart, Thibaut <
>> t.jombart at imperial.ac.uk
>> > wrote:
>>
>> >
>> >
>> > What does nrow(F1) and other nrow(...)'s say?
>> >
>> >
>> >
>> >
>> > ------------------------------
>> > *From:* Spencer Bruce [goatsrunfaster at gmail.com]
>> > *Sent:* 23 October 2014 15:52
>> > *To:* Jombart, Thibaut
>> > *Cc:* adegenet-forum at lists.r-forge.r-project.org
>> > *Subject:* Re: [adegenet-forum] repooling random rows from genind
>> objects
>> >
>> > Error message:
>> >
>> > Error in sample.int(length(x), size, replace, prob) :
>> > invalid first argument
>> >
>> > On Thu, Oct 23, 2014 at 10:50 AM, Jombart, Thibaut <
>> > t.jombart at imperial.ac.uk> wrote:
>> >
>> >>
>> >> Hello,
>> >> hard to figure out what is wrong without the error message..
>> >> 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
>> Spencer
>> >> Bruce [goatsrunfaster at gmail.com]
>> >> *Sent:* 23 October 2014 15:29
>> >> *To:* adegenet-forum at lists.r-forge.r-project.org
>> >> *Subject:* [adegenet-forum] repooling random rows from genind objects
>> >>
>> >> Hello All!
>> >>
>> >> I have three seperate populations as genind objects. What I would like
>> >> to do is pull a certain number of random individuals from each, to
>> form a
>> >> new single genind population.
>> >>
>> >> I would then like individuals from this new genind population to mate
>> >> randomly, producing another genind object which would contain their
>> >> offspring.
>> >>
>> >> Below is the code I came up with (which does not work):
>> >>
>> >> Year1 <- repool(F1[sample(nrow(F1), 500), ], pop1[sample(nrow(pop1),
>> >> 750), ], pop2[sample(nrow(pop2), 750), ], n=2000)
>> >>
>> >> Year2 <- hybridize(Year1[sample(nrow(Year1), 1000), ],
>> >> Year1[sample(nrow(Year1), 1000), ], n=2000)
>> >>
>> >>
>> >> any help would be greatly appreciated!
>> >>
>> >> Best,
>> >> Spencer
>> >>
>> >> --
>> >> Spencer A Bruce
>> >> 200 Washington St.
>> >> Troy, NY 12180
>> >> 518 225 0787
>> >>
>> >
>> >
>> >
>> > --
>> > Spencer A Bruce
>> > 200 Washington St.
>> > Troy, NY 12180
>> > 518 225 0787
>> >
>>
>>
>>
>> --
>> Spencer A Bruce
>> 200 Washington St.
>> Troy, NY 12180
>> 518 225 0787
>> -------------- next part --------------
>> An HTML attachment was scrubbed...
>> URL: <
>> http://lists.r-forge.r-project.org/pipermail/adegenet-forum/attachments/20141023/c51ccf09/attachment.html
>> >
>>
>> ------------------------------
>>
>> _______________________________________________
>> adegenet-forum mailing list
>> adegenet-forum at lists.r-forge.r-project.org
>>
>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/adegenet-forum
>>
>> End of adegenet-forum Digest, Vol 74, Issue 9
>> *********************************************
>>
>
>
> _______________________________________________
> adegenet-forum mailing list
> adegenet-forum at lists.r-forge.r-project.org
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/adegenet-forum
>
--
Spencer A Bruce
200 Washington St.
Troy, NY 12180
518 225 0787
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.r-forge.r-project.org/pipermail/adegenet-forum/attachments/20141024/904575eb/attachment-0001.html>
More information about the adegenet-forum
mailing list