[adegenet-forum] Inbreeding coefficient calculation by adegenet

[Jombart, Thibaut]

Hello, 

I can't seem to read your data using the command line provided:
####
> toto<-read.structure(file="finalFiltered_noLowCov_e0_LOCUS_10.stru",n.ind=154,n.loc=43231,onerowperind=FALSE,col.lab=1,row.marknames=1,NA.char="-9",missing=0)

 Which column contains the population factor ('0' if absent)? 2

 Which other optional columns should be read (press 'return' when done)? 1: 

 Converting data from a STRUCTURE .stru file to a genind object... 

Error in txt[(lastline - n + 1):lastline] : 
  only 0's may be mixed with negative subscripts
####

Less individuals in the sample data maybe?

Cheers
Thibaut

--
######################################
Dr Thibaut JOMBART
MRC Centre for Outbreak Analysis and Modelling
Department of Infectious Disease Epidemiology
Imperial College - School of Public Health
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 Tohamy Yousef [tohamyy at yahoo.com]
Sent: 18 December 2013 08:44
To: adegenet-forum at lists.r-forge.r-project.org
Subject: [adegenet-forum] Inbreeding coefficient calculation by adegenet

Dear Dr. Jombart,
I am trying to calculate the inbreeding coefficient for two populations (US=81 and IP=73)  with 43231 SNPs. I am using your your manual, an introduction to adgenet 1.4-0, but I have a problem in the calculation. It gives me an error message:
Error in sample.int(length(x), size, replace, prob) :
  NA in probability vector
I do not know why? I did it as following:

> toto<-read.structure(file="finalFiltered_noLowCov_e0_LOCUS_POP.stru",n.ind=154,n.loc=43231,onerowperind=FALSE,col.lab=1,row.marknames=1,NA.char="-9",missing=0)
 Which column contains the population factor ('0' if absent)? 2

 Which other optional columns should be read (press 'return' when done)? 1:
 Converting data from a STRUCTURE .stru file to a genind object...
> is.genind(toto)
[1] TRUE
> toto$pop.names
  P1   P2
"US" "IP"
> sa1<- seppop(toto)$US
> sa1
   #####################
   ### Genind object ###
   #####################
- genotypes of individuals -
S4 class:  genind
@call: .local(x = x, i = i, j = j, treatOther = ..1, quiet = ..2, drop = drop)
@tab:  81 x 61169 matrix of genotypes
@ind.names: vector of  81 individual names
@loc.names: vector of  43231 locus names
@loc.nall: number of alleles per locus
@loc.fac: locus factor for the  61169 columns of @tab
@all.names: list of  43231 components yielding allele names for each locus
@ploidy:  2
@type:  codom
Optionnal contents:
@pop:  factor giving the population of each individual
@pop.names:  factor giving the population of each individual
@other: a list containing: elements without names

> temp1<- inbreeding(sa1, N=81)
Error in sample.int(length(x), size, replace, prob) :
  NA in probability vector

> sa2<- seppop(toto)$IP
> sa2
   #####################
   ### Genind object ###
   #####################
- genotypes of individuals -
S4 class:  genind
@call: .local(x = x, i = i, j = j, treatOther = ..1, quiet = ..2, drop = drop)
@tab:  73 x 61169 matrix of genotypes
@ind.names: vector of  73 individual names
@loc.names: vector of  43231 locus names
@loc.nall: number of alleles per locus
@loc.fac: locus factor for the  61169 columns of @tab
@all.names: list of  43231 components yielding allele names for each locus
@ploidy:  2
@type:  codom
Optionnal contents:
@pop:  factor giving the population of each individual
@pop.names:  factor giving the population of each individual
@other: a list containing: elements without names

> temp2<- inbreeding(sa2, N=73)
Error in sample.int(length(x), size, replace, prob) :
  NA in probability vector


Could you please tell me how can I fix this problem?
I attached you a part of my data. and I hope that  help me.

Thank you advance
Best regards,
Tohamy
-------------------------------------------
Eltohamy Yousef  M.Sc.
Crop Biodiversity and Breeding Informatics
Institute of Plant Breeding, Seed Science and Population Genetics (350)
University of Hohenheim
Fruwirtstrasse 21, 70599 Stuttgart
Office phone:0049711 459-24437
Email: tohamyy at yahoo.com
            E.yousef at uni-hohenheim.de
            tohamy_yousef at agr.suez.edu.eg
Web.www.evoplant.uni-hohenheim.de