<html><body><div style="color:#000; background-color:#fff; font-family:HelveticaNeue, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif;font-size:10pt"><div style="" class=""><br style=""></div><div style="" class="" id="yiv5207489138yui_3_13_0_ym1_7_1395406268939_24"><span style="" class="" id="yiv5207489138yui_3_13_0_ym1_7_1395406268939_31">Dear Dr. Jombart</span></div><span style="" class="" id="yiv5207489138yui_3_13_0_ym1_7_1395406268939_31">Firsst of all, I am sorry for disrupting you again. But, really I need your help. I
wrote you
before and asked about inbreeding calculation. You suggested that I use
less number of markers and other advices. SO, I tried to follow all your comments. For example I decided to use only
2247 SNP markers without missing data (before I had 43231 with missing
data).</span> But I am trying a lot and still have the same problem.<br> I am attaching to you the new data (new_inbreeding.stru). <br><br><br>Thanks in advance.<br style="" class="" clear="none"><br style="" class="" clear="none">######### my script<br style="" class="" clear="none"><br style="" class="" clear="none">> library(adegenet)<br style="" class="" clear="none">>
toto<-read.structure(file="new_inbreeding.stru",n.ind=154,n.loc=2247,onerowperind=FALSE,col.lab=1,row.marknames=1,NA.char="-9",missing="mean")<br style="" class="" clear="none"><br style="" class="" clear="none">Which column contains the population factor ('0' if absent)? 2<br style="" class="" clear="none"><br style="" class="" clear="none"> Which other optional columns should be read (press 'return' when done)? 1: <br style="" class="" clear="none">> toto<br style="" class="" clear="none"><br style="" class="" clear="none"> #####################<br style="" class="" clear="none"> ### Genind object ### <br style="" class="" clear="none"> #####################<br style="" class="" clear="none">- genotypes of individuals - <br style="" class="" clear="none"><br style="" class="" clear="none">S4 class: genind<br style="" class="" clear="none">@call: read.structure(file = "inbreeding.stru", <br style=""
class="" clear="none"> n.ind = 154, n.loc = 2247, onerowperind = FALSE, col.lab = 1, <br style="" class="" clear="none"> row.marknames = 1, NA.char = "-9", missing =
"mean")<br style="" class="" clear="none"><br style="" class="" clear="none">@tab: 154 x 3610 matrix of genotypes<br style="" class="" clear="none"><br style="" class="" clear="none">@ind.names: vector of 154 individual names<br style="" class="" clear="none">@loc.names: vector of 2247 locus names<br style="" class="" clear="none">@loc.nall: number of alleles per locus<br style="" class="" clear="none">@loc.fac: locus factor for the 3610 columns of @tab<br style="" class="" clear="none">@all.names: list of 2247 components yielding allele names for each locus<br style="" class="" clear="none">@ploidy: 2<br style="" class="" clear="none">@type: codom<br style="" class="" clear="none"><br style="" class="" clear="none">Optionnal contents: <br style="" class="" clear="none">@pop: factor giving the population of each individual<br style="" class="" clear="none">@pop.names: factor giving the population of
each individual<br style="" class="" clear="none"><br style="" class="" clear="none">@other: - empty -<br style="" class="" clear="none">> toto$pop.names<br style="" class="" clear="none"> P1 P2 <br style="" class="" clear="none">"US" "IP" <br style="" class="" clear="none">>U<- seppop(toto)$US<br style="" class="" clear="none">> U<br style="" class="" clear="none"><br style="" class="" clear="none"> #####################<br style="" class="" clear="none"> ### Genind object ### <br style="" class="" clear="none"> #####################<br style="" class="" clear="none">- genotypes of individuals - <br style="" class="" clear="none"><br style="" class="" clear="none">S4 class: genind<br style="" class="" clear="none">@call: .local(x = x, i = i, j = j, treatOther = ..1, quiet = ..2, drop = drop)<br style="" class="" clear="none"><br style="" class="" clear="none">@tab: 81 x
3610 matrix of genotypes<br style="" class="" clear="none"><br style="" class="" clear="none">@ind.names: vector of 81 individual names<br style="" class="" clear="none">@loc.names: vector of 2247 locus names<br style="" class="" clear="none">@loc.nall: number of alleles per locus<br style="" class="" clear="none">@loc.fac: locus factor for the 3610 columns of @tab<br style="" class="" clear="none">@all.names: list of 2247 components yielding allele names for each locus<br style="" class="" clear="none">@ploidy: 2<br style="" class="" clear="none">@type: codom<br style="" class="" clear="none"><br style="" class="" clear="none">Optionnal contents: <br style="" class="" clear="none">@pop: factor giving the population of each individual<br style="" class="" clear="none">@pop.names: factor giving the population of each individual<br style="" class="" clear="none"><br style="" class="" clear="none">@other: a
list containing: elements without names <br style="" class="" clear="none"><br style="" class="" clear="none">> U1<- inbreeding(U, N=100)<br style="" class="" clear="none"><span class="" style="color:rgb(255, 255, 255)"><span class="" style="background-color:rgb(205, 35, 44)">Error in sample.int(length(x), size, replace, prob) : <br style="" class="" clear="none"> NA in probability vector</span></span><div style="color: rgb(255, 255, 255); font-size: 13.3333px; font-family: HelveticaNeue,Helvetica Neue,Helvetica,Arial,Lucida Grande,sans-serif; background-color: transparent; font-style: normal;" class=""><span style="" class=""></span></div><div style="" class=""> </div></div></body></html>