[adegenet-forum] adegenet-forum Digest, Vol 55, Issue 2

[Roy Mathew Francis]

Adegenet can already read genalex format.
This is what you do

The microsatellite data and the coordinate data separately as separate text files.
The microsatellite data is exported from GenAlex as 'genclass' file (x.gen) and read into R using read.genepop.
The coordinates are read in as regular tab delimited file and then added to the genindtype object.

df<-read.genepop("Microsatellites.gen", missing="mean")

x<-as.matrix(read.table("coordinates.txt"))
df at other<-list(xy=x)


Regards
Roy Mathew Francis
From: adegenet-forum-bounces at lists.r-forge.r-project.org [mailto:adegenet-forum-bounces at lists.r-forge.r-project.org] On Behalf Of Zhian Kamvar
Sent: 26 March 2013 18:23
To: adegenet-forum at lists.r-forge.r-project.org; rita.castil at gmail.com
Subject: Re: [adegenet-forum] adegenet-forum Digest, Vol 55, Issue 2

Hi Rita,

I am actually writing an R package that uses the genind format and I have written a function that will import genalex formatted files called read.genalex. You can find instructions for installation here: https://github.com/poppr/poppr
If you want to just use the raw code, you can download it here (the function starts at line 180 and finishes at line 319): https://github.com/poppr/poppr/blob/master/R/file_handling.r
Once you have the package installed or the source code in your R session, you can import your genalex file using:
read.genalex("myfile.csv", geo=TRUE)
Hope that helps!

Cheers,
Zhian

On Tue, Mar 26, 2013 at 4:00 AM, <adegenet-forum-request at lists.r-forge.r-project.org<mailto:adegenet-forum-request at lists.r-forge.r-project.org>> wrote:
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Today's Topics:

   1.  inexperienced user (Rita Castilho)


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Message: 1
Date: Mon, 25 Mar 2013 16:15:13 +0000
From: Rita Castilho <rita.castil at gmail.com<mailto:rita.castil at gmail.com>>
To: adegenet-forum at lists.r-forge.r-project.org<mailto:adegenet-forum at lists.r-forge.r-project.org>
Subject: [adegenet-forum]  inexperienced user
Message-ID: <51507811.7060804 at gmail.com<mailto:51507811.7060804 at gmail.com>>
Content-Type: text/plain; charset="iso-8859-1"; Format="flowed"

Hi!
I have a simple question. Most of us have our microsatellite data in an
excel file to start with. The ones how use GenAlex even have the
geographic coordinates in the last two rows. We can easily convert the
data in the sheet into several formats. How can I convert an easily
obtained csv file with headers (1sr row = individual id, 2nd =
population id, 3rd row= allele 1, locus 1, 4th row= allele 2, locus 1,
etc, 17th row = latitude, 18th row = longitude) nto a genind object that
can be used in sPCA? I get an error that coordinates are repeated, but
that is normal as there are multiple individuals in the same pop.

If this question was answered previously, I will appreciate if you could
direct me to it.
Many thanks
Rita

first 5 rows of test.csv file
ind,pop,loc1A,loc1B,loc2A,loc2B,loc3A,loc3B,loc4A,loc4B,loc5A,loc5B,loc6A,loc6B,loc7A,loc7B,lat,long
FD_01,FD,151,163,168,170,189,201,248,248,177,187,166,166,230,246,49.85,-29.62
FD_02,FD,137,147,146,146,173,181,240,254,177,179,162,166,230,246,49.85,-29.62
FD_03,FD,137,169,146,168,173,173,222,238,193,203,164,164,230,246,49.85,-29.62
FD_04,FD,137,147,144,144,189,201,236,242,185,193,166,166,238,240,49.85,-29.62

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