[adegenet-forum] AFLP data format
Jombart, Thibaut
t.jombart at imperial.ac.uk
Mon Dec 6 00:42:50 CET 2010
Dear Russell,
it would have been more informative to explain what your problem exactly was in the first place.
You need to provide a matrix of genetic data only to genind, and set the population information separately.
For instance:
###
myPop <- factor(dat$pop)
dat <- dat[,-1]
obj <- genind(dat, ploidy=1, type="PA")
pop(obj) <- myPop
###
Cheers
Thibaut
________________________________________
From: adegenet-forum-bounces at lists.r-forge.r-project.org [adegenet-forum-bounces at lists.r-forge.r-project.org] On Behalf Of Pfau, Dr. Russell S. [PFAU at tarleton.edu]
Sent: 05 December 2010 23:25
To: adegenet-forum at lists.r-forge.r-project.org
Subject: Re: [adegenet-forum] AFLP data format
I do appreciate your help...
I had already read the section on presence/absence, and did see the aflp dataset. And, I can load data *without* the population designation column. However, I cannot seem to load a dataset with the 2nd column designating populations. I've read the ?read.table help but found no answers there. It thinks the 2nd column is a column of alleles (see below...there are 4 loci, but it thinks there are 5).
I think my problem is that I do not know how to use the 'pop' argument in the 'genind' command, below:
pop a factor giving the population of each genotype in 'x'
Here are my attempts:
> dat <- read.table("aflp2.txt", header = TRUE)
> dat
pop loc1 loc2 loc3 loc4
indA pop1 1 0 1 1
indB pop1 0 1 1 1
indC pop1 1 1 0 1
indD pop2 0 1 1 1
indE pop2 1 1 0 0
indF pop2 1 0 1 1
indG pop2 0 1 1 0
> obj <-genind(dat, ploidy=2, type="PA")
> obj
#####################
### Genind object ###
#####################
- genotypes of individuals -
S4 class: genind
@call: genind(tab = dat, ploidy = 2, type = "PA")
@tab: 7 x 5 matrix of genotypes
@ind.names: vector of 7 individual names
@loc.names: vector of 5 locus names
@loc.nall: NULL
@loc.fac: NULL
@all.names: NULL
@ploidy: 2
@type: PA
Optionnal contents:
@pop: - empty -
@pop.names: - empty -
@other: - empty -
>
> obj <-genind(dat, ploidy=2, type="PA", pop=dat at pop)
Error in genind(dat, ploidy = 2, type = "PA", pop = dat at pop) :
trying to get slot "pop" from an object (class "data.frame") that is not an S4 object
>
> obj <-genind(dat, ploidy=2, type="PA", pop=truenames(dat)$pop)
Error in function (classes, fdef, mtable) :
unable to find an inherited method for function "truenames", for signature "data.frame"
>
> obj <-genind(dat, ploidy=2, type="PA", pop = dat$pop)
> obj
#####################
### Genind object ###
#####################
- genotypes of individuals -
S4 class: genind
@call: genind(tab = dat, pop = dat$pop, ploidy = 2, type = "PA")
@tab: 7 x 5 matrix of genotypes
@ind.names: vector of 7 individual names
@loc.names: vector of 5 locus names
@loc.nall: NULL
@loc.fac: NULL
@all.names: NULL
@ploidy: 2
@type: PA
Optionnal contents:
@pop: factor giving the population of each individual
@pop.names: factor giving the population of each individual
@other: - empty -
>
________________________________________
From: Jombart, Thibaut [t.jombart at imperial.ac.uk]
Sent: Sunday, December 05, 2010 3:00 PM
To: Pfau, Dr. Russell S.; adegenet-forum at lists.r-forge.r-project.org
Subject: RE: AFLP data format
Dear Russell,
I am afraid you have been viewing an outdated version of the tutorial.
In the current version, there is a section titled "Handling presence/absence data" (section 3.13, p.49), which exactly answers your question, with a fake AFLP dataset remarkably similar to your data formatted as a table.
Best
Thibaut
--
######################################
Dr Thibaut JOMBART
MRC Centre for Outbreak Analysis and Modelling
Department of Infectious Disease Epidemiology
Imperial College - Faculty of Medicine
St Mary’s Campus
Norfolk Place
London W2 1PG
United Kingdom
Tel. : 0044 (0)20 7594 3658
t.jombart at imperial.ac.uk
http://sites.google.com/site/thibautjombart/
http://adegenet.r-forge.r-project.org/
________________________________________
From: adegenet-forum-bounces at lists.r-forge.r-project.org [adegenet-forum-bounces at lists.r-forge.r-project.org] On Behalf Of Pfau, Dr. Russell S. [PFAU at tarleton.edu]
Sent: 04 December 2010 03:03
To: adegenet-forum at lists.r-forge.r-project.org
Subject: [adegenet-forum] AFLP data format
I have spent the past 5 hours reading the adegenet manual, tutorial, and forum and have yet to learn how to put my AFLP data into a file like the nancycats.RData file for use in analysis with adegenet. How on earth does one do this?
I have my data in two format types, and have created simple test files showing the two format types that I have (see below). Please help....where do I go from here!
Russell
table format:
loc1 loc2 loc3 loc4
indA pop1 1 0 1 1
indB pop1 0 1 1 1
indC pop1 1 1 0 1
indD pop2 0 1 1 1
indE pop2 1 1 0 0
indF pop2 1 0 1 1
indG pop2 0 1 1 0
STRUCTURE format:
loc1 loc2 loc3 loc4
indA pop1 1 0 1 1
indA pop1 1 0 1 1
indB pop1 0 1 1 1
indB pop1 0 1 1 1
indC pop1 1 1 0 1
indC pop1 1 1 0 1
indD pop2 0 1 1 1
indD pop2 0 1 1 1
indE pop2 1 1 0 0
indE pop2 1 1 0 0
indF pop2 1 0 1 1
indF pop2 1 0 1 1
indG pop2 0 1 1 0
indG pop2 0 1 1 0
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