[adegenet-forum] Problem converting structure file to genind (length of 'dimnames' [2] not equal to array extent)

[Charlotte Hurry]

Hello
I have been trying to convert my structure file to a genind object but I am
having some issues.  I am getting this error and I can't find an
appropriate fix.  I have looked through forum history and found a similar
issue but the fix suggested didn't work for me.

my file looks like this:
Ind    Pop    tb109    tb117    tb129    tb130    tb136    tb187    tb188
GM4_283    1    118    108    132    125    122    168    159
GM4_283    1    120    112    138    129    122    176    168
GM336    1    114    112    128    123    124    168    0
GM336    1    116    112    136    123    128    176    0
GM337    1    0    110    126    123    126    168    159
GM337    1    0    112    126    123    126    176    174
E276    2    118    108    0    0    122    166    165
E276    2    118    112    0    0    122    176    190
E277    2    116    108    126    119    124    168    159
E277    2    118    112    138    129    128    176    174
E278    2    114    108    124    121    122    168    162
E278    2    114    112    126    125    128    176    180

I used the script
*> tems<-read.structure("TBtest1.str",row.marknames=1,onerowperind=FALSE,
n.ind=190, n.loc=7, col.lab=1, col.pop=2, ask=TRUE)*

Which brings up the following message, and I press RETURN:


* Which other optional columns should be read (press 'return' when done)?
1:  Converting data from a STRUCTURE .stru file to a genind object... *

Then get this error:



*Error in `colnames<-`(`*tmp*`, value = c("Ind", "Pop", "tb109", "tb117",
:   length of 'dimnames' [2] not equal to array extent*
Has anybody got a fix to get my original STRUCTURE file to work as a Genind
object.?

As an aside, on the forum I found a work around under the title "Trouble
converting to genid object", which converts a read.table document into
genind which I followed and I got this error:
Warning message:
In .local(.Object, ...) : NAs introduced by coercion
and this file:
> head(as.matrix(obj1))
    V1 V2  V3  V4  V5  V6  V7  V8  V9
001 NA NA  NA  NA  NA  NA  NA  NA  NA
002 NA  1 118 108 132 125 122 168 159
003 NA  1 120 112 138 129 122 176 168
004 NA  1 114 112 128 123 124 168   0
005 NA  1 116 112 136 123 128 176   0
006 NA  1   0 110 126 123 126 168 159

So i would like a different solution to my problem if possible.
Many thanks
Charlotte


Charlotte
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