[adegenet-forum] unable to import a diploid dataset using read.strucutre

Jombart, Thibaut t.jombart at imperial.ac.uk
Mon Dec 30 10:42:18 CET 2013


Hello, 

the file seems to contain one column to many. 
> x <- read.table("temp/14loci.stru",skip=1)
> head(x)
     V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 V11 V12 V13 V14 V15 V16 V17 V18 V19 V20 V21
1 QCS10  1  0  2  2 -9 -9 -9 -9  -9  -9   2   2   2   2   1   1  -9  -9   1   2
2 QCS13  1  0  2  2 -9 -9  2  2  -9  -9  -9  -9   2   2  -9  -9   1   1   2   2
3 QCS16  1  0  2  2 -9 -9 -9 -9   1   1   2   2   2   2  -9  -9   1   1   2   2
4 QCS19  1  0 -9 -9  2  8  2  2   1   1   2   2   2   2   1   1   1   1   2   2
5 QCS22  1  0 -9 -9  2  2  2  2   1   1   2   2  -9  -9  -9  -9   1   1   2   2
6  QCS4  1  0  2  2  1  1  2  2  -9  -9   2   2   1   2   1   1  -9  -9  -9  -9
  V22 V23 V24 V25 V26 V27 V28 V29 V30 V31
1   1   2   1   1   1   1   1   1   1   1
2   1   1   1   3   3   3   1   1   1   1
3   1   1   1   1   1   3   1   1   1   1
4  -9  -9   1   1  -9  -9   1   1   1   1
5   1   1   3   3   1   3   1   1   1   1
6   1   1   1   3   3   3   1   1   1   1
> 

Here, there should be 30 columns and not 31.

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 sun-ye at scib.ac.cn [sun-ye at scib.ac.cn]
Sent: 30 December 2013 03:09
To: adegenet-forum at lists.r-forge.r-project.org
Subject: [adegenet-forum] unable to import a diploid dataset using      read.strucutre

Dear

      I am unable to import a diploid dataset using read.strucutre.  I always got an error:

Converting data from a STRUCTURE .stru file to a genind object...
df2genind(X = X, pop = pop, missing = missing, ploidy = 2) :
  2 alleles cannot be coded by a total of 3 characters

I paste data (104 individual, 14 loci), Can you help fix this?
RADid_0000113 RADid_0000114 RADid_0000250 RADid_0000388 RADid_0000798 RADid_0001205 RADid_0001522 RADid_0001584 RADid_0001771 RADid_0002962 RADid_0003463 RADid_0003558 RADid_0004239 RADid_0004366
QCS10 1 0 2 2 -9 -9 -9 -9 -9 -9 2 2 2 2 1 1 -9 -9 1 2 1 2 1 1 1 1 1 1 1 1
QCS13 1 0 2 2 -9 -9 2 2 -9 -9 -9 -9 2 2 -9 -9 1 1 2 2 1 1 1 3 3 3 1 1 1 1
QCS16 1 0 2 2 -9 -9 -9 -9 1 1 2 2 2 2 -9 -9 1 1 2 2 1 1 1 1 1 3 1 1 1 1
QCS19 1 0 -9 -9 2 8 2 2 1 1 2 2 2 2 1 1 1 1 2 2 -9 -9 1 1 -9 -9 1 1 1 1
QCS22 1 0 -9 -9 2 2 2 2 1 1 2 2 -9 -9 -9 -9 1 1 2 2 1 1 3 3 1 3 1 1 1 1
QCS4 1 0 2 2 1 1 2 2 -9 -9 2 2 1 2 1 1 -9 -9 -9 -9 1 1 1 3 3 3 1 1 1 1
QCS7 1 0 2 2 2 2 2 2 1 1 2 2 -9 -9 1 1 1 1 2 2 1 1 1 1 2 3 1 1 1 1
QCSI 1 0 1 1 -9 -9 2 2 1 1 2 2 2 2 1 1 -9 -9 2 2 1 1 3 3 3 3 1 9 -9 -9
EM13 2 0 2 2 -9 -9 2 11 -9 -9 2 2 2 2 1 1 1 1 2 2 1 1 1 1 1 3 1 1 1 1
EM16 2 0 1 1 2 2 -9 -9 1 1 2 2 2 2 1 1 1 1 1 2 1 1 1 1 1 1 1 1 -9 -9
EM19 2 0 -9 -9 2 2 2 6 1 1 2 2 2 2 -9 -9 1 1 2 2 -9 -9 1 3 1 3 1 1 1 1
EM20 2 0 -9 -9 2 2 2 4 1 1 2 2 2 2 -9 -9 1 1 2 2 1 1 1 1 1 1 1 1 1 2
EM22 2 0 2 2 2 2 -9 -9 1 1 2 2 1 2 1 1 1 1 2 2 1 1 1 1 1 1 1 1 1 1
EM24 2 0 -9 -9 -9 -9 2 2 1 1 2 2 1 2 -9 -9 1 1 1 2 1 1 1 1 1 1 1 1 1 1
EM4 2 0 2 2 2 2 2 2 1 1 2 2 2 2 1 1 1 1 1 2 1 1 1 1 3 3 1 1 1 9
EM8 2 0 2 2 2 2 -9 -9 1 1 2 2 -9 -9 1 1 1 1 1 2 1 1 1 3 3 3 1 1 1 1
SF10 3 0 2 2 2 2 -9 -9 1 1 2 2 2 2 1 1 -9 -9 1 1 1 2 1 1 1 1 1 1 -9 -9
SF13 3 0 2 2 2 2 2 2 1 1 2 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
SF16 3 0 -9 -9 2 2 2 10 1 1 2 2 2 2 1 1 -9 -9 1 1 1 1 3 6 1 1 1 8 1 1
SF19 3 0 2 2 2 2 2 2 1 1 -9 -9 -9 -9 1 1 1 1 1 1 1 1 1 1 -9 -9 1 1 1 1
SF1 3 0 -9 -9 2 2 2 2 1 1 2 2 2 2 1 1 1 1 1 2 1 1 1 1 1 1 1 1 1 1
SF22 3 0 -9 -9 2 2 2 10 1 1 2 2 -9 -9 1 1 1 1 1 2 1 1 1 1 -9 -9 1 1 1 1
SF4 3 0 2 2 2 2 1 1 1 1 2 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 -9 -9
SF7 3 0 -9 -9 2 2 -9 -9 1 1 2 2 1 1 1 1 1 1 1 2 1 2 1 1 1 1 1 1 1 2
TTS10 4 0 -9 -9 2 2 1 1 1 1 2 2 2 2 -9 -9 1 1 1 1 1 1 1 1 -9 -9 1 6 1 1
TTS13 4 0 2 2 2 2 2 2 1 1 2 2 2 2 1 1 1 1 1 1 1 4 -9 -9 -9 -9 1 1 1 1
TTS16 4 0 1 2 1 1 1 2 1 1 1 2 1 1 -9 -9 1 2 1 1 1 1 1 1 1 2 1 1 1 1
TTS1 4 0 -9 -9 2 2 -9 -9 1 1 2 2 1 2 1 1 -9 -9 1 1 1 1 1 1 1 3 1 1 1 1
TTS22 4 0 -9 -9 2 2 1 1 1 1 2 2 1 2 1 1 1 1 1 1 1 3 1 1 1 1 1 1 1 1
TTS24 4 0 2 2 1 1 2 2 1 1 2 2 2 2 -9 -9 1 1 2 2 1 1 1 5 -9 -9 1 1 1 1
TTS5 4 0 -9 -9 2 2 2 2 1 1 2 2 2 2 1 1 1 2 1 1 1 5 1 1 -9 -9 1 3 1 1
TTS7 4 0 2 2 2 2 2 2 1 1 -9 -9 2 2 1 1 1 1 1 1 1 1 -9 -9 2 2 1 1 1 1
JYS10 5 0 2 2 2 2 -9 -9 1 1 2 2 1 2 1 1 1 3 1 2 7 7 1 1 1 1 1 1 1 2
JYS13 5 0 2 3 2 2 2 2 1 1 2 7 1 1 -9 -9 1 2 2 2 1 1 1 1 2 2 1 1 2 2
JYS16 5 0 -9 -9 2 2 2 2 1 1 2 6 1 2 1 1 3 10 1 1 1 1 1 1 1 2 1 7 -9 -9
JYS19 5 0 1 1 2 2 -9 -9 1 1 2 2 1 1 -9 -9 3 3 1 1 1 1 1 1 3 3 1 1 1 1
JYS1 5 0 1 1 2 2 1 1 1 1 2 2 1 1 -9 -9 1 1 -9 -9 1 8 1 1 1 1 1 1 1 1
JYS22 5 0 2 2 -9 -9 2 2 1 7 2 2 -9 -9 1 1 1 1 -9 -9 -9 -9 1 1 3 3 1 1 1 1
JYS4 5 0 -9 -9 2 2 -9 -9 1 1 2 2 -9 -9 1 1 2 2 2 2 1 1 1 4 2 2 1 1 -9 -9
JYS7 5 0 2 2 2 2 -9 -9 1 1 2 2 2 2 1 1 2 3 -9 -9 1 1 1 1 1 1 1 1 1 1
XC11 6 0 -9 -9 2 2 2 2 1 8 2 2 1 2 -9 -9 -9 -9 1 2 -9 -9 1 1 1 2 1 1 1 2
XC14 6 0 -9 -9 2 2 2 2 1 8 2 2 1 1 -9 -9 1 1 2 2 1 1 1 1 1 1 1 1 1 1
XC17 6 0 -9 -9 2 2 2 2 1 1 2 2 1 1 -9 -9 1 1 2 2 1 1 1 1 1 1 1 1 1 1
XC1 6 0 -9 -9 2 2 2 2 -9 -9 2 2 1 1 -9 -9 -9 -9 1 1 -9 -9 1 1 1 1 1 1 1 1
XC3 6 0 -9 -9 2 2 2 2 1 8 2 2 1 2 -9 -9 1 1 2 2 1 1 1 1 1 2 1 1 1 2
XC5 6 0 -9 -9 2 2 2 2 1 1 2 2 1 1 -9 -9 -9 -9 2 2 -9 -9 1 1 1 1 1 1 1 1
XC7 6 0 -9 -9 2 2 2 2 1 1 2 2 1 1 -9 -9 -9 -9 1 1 1 1 1 1 1 1 1 1 1 1
XC9 6 0 -9 -9 2 2 2 2 1 1 2 2 -9 -9 -9 -9 -9 -9 1 5 -9 -9 1 1 1 1 1 1 1 1
FJS10 7 0 1 1 1 2 2 2 1 1 2 2 2 2 -9 -9 3 3 1 1 1 1 -9 -9 3 3 1 1 2 2
FJS13 7 0 1 1 1 1 2 2 1 1 2 2 1 1 2 2 9 9 1 1 1 3 1 1 3 3 1 1 1 2
FJS16 7 0 1 1 1 2 2 2 1 1 2 2 1 2 1 1 1 1 1 1 1 3 1 1 3 3 1 1 2 2
FJS19 7 0 -9 -9 1 1 2 2 1 1 2 2 2 2 1 1 1 1 1 1 1 1 1 1 3 3 1 1 2 2
FJS1 7 0 1 1 1 1 -9 -9 1 1 2 2 1 1 1 1 1 1 1 1 1 1 1 1 3 3 1 1 1 2
FJS22 7 0 1 1 1 1 2 2 1 1 2 2 2 2 1 1 1 1 1 1 1 1 -9 -9 -9 -9 1 1 -9 -9
FJS4 7 0 1 1 1 2 -9 -9 1 1 2 2 2 2 1 1 1 3 1 1 1 1 1 1 -9 -9 1 1 1 1
FJS7 7 0 1 1 1 1 2 2 1 1 2 2 1 1 1 2 1 9 1 1 1 1 1 1 -9 -9 1 1 2 2
DYS11 8 0 1 1 1 1 2 2 1 1 2 2 2 2 1 1 1 1 1 1 1 1 1 2 3 3 1 1 2 2
DYS15 8 0 1 1 1 1 2 2 1 1 2 2 1 2 1 1 1 1 1 1 1 1 1 1 3 3 1 1 2 2
DYS1 8 0 1 1 1 2 2 3 1 1 2 2 2 2 1 1 1 1 1 1 1 1 1 2 3 3 1 2 2 2
DYS21 8 0 1 1 1 1 2 2 1 1 2 2 2 2 1 1 1 1 1 1 1 3 1 2 3 3 1 1 -9 -9
DYS3 8 0 1 1 1 1 2 2 1 1 2 2 1 2 1 1 1 1 1 1 1 1 1 2 3 3 1 1 2 2
DYS5 8 0 1 1 1 1 2 6 1 1 -9 -9 1 2 1 1 1 1 1 1 1 1 1 2 3 3 1 1 2 2
DYS7 8 0 1 1 1 1 2 2 1 4 2 2 2 2 1 1 1 7 1 1 1 1 1 2 3 3 1 1 2 2
DYS9 8 0 1 1 1 1 -9 -9 1 1 2 8 2 2 1 1 1 1 1 1 1 1 1 2 3 3 1 1 2 2
JGS11 9 0 -9 -9 2 2 5 5 1 1 -9 -9 1 1 2 2 1 1 1 1 -9 -9 1 2 -9 -9 1 3 1 1
JGS13 9 0 1 1 2 2 2 2 1 1 2 3 1 1 2 2 1 4 1 1 3 3 1 2 -9 -9 1 3 1 1
JGS16 9 0 1 1 2 2 2 2 1 1 3 3 1 1 2 2 1 1 1 1 3 3 1 2 3 3 1 3 1 1
JGS1 9 0 1 1 2 11 5 5 1 1 3 3 1 1 2 2 4 4 1 1 1 1 1 2 3 3 1 3 1 1
JGS3 9 0 1 1 2 2 -9 -9 1 1 2 3 1 1 2 2 4 4 1 1 -9 -9 1 2 -9 -9 1 3 1 1
JGS5 9 0 1 1 2 2 5 5 1 1 2 3 1 1 2 2 1 1 1 1 -9 -9 1 2 3 3 1 3 1 1
JGS7 9 0 1 1 2 2 -9 -9 1 1 3 3 1 1 2 2 -9 -9 1 1 3 3 1 2 3 3 3 3 1 1
JGS9 9 0 -9 -9 -9 -9 2 5 1 1 3 3 1 1 2 2 -9 -9 1 1 -9 -9 1 1 -9 -9 3 3 1 1
GT11 10 0 1 1 2 9 2 8 1 1 2 3 1 4 2 2 1 4 1 1 1 3 -9 -9 -9 -9 1 1 1 2
GT13 10 0 1 1 2 6 7 8 3 3 -9 -9 1 1 1 2 4 4 1 6 3 3 2 2 3 3 4 4 1 6
GT17 10 0 1 1 2 2 7 7 3 3 2 2 1 9 1 1 1 4 1 1 1 3 -9 -9 3 3 1 1 -9 -9
GT19 10 0 1 1 2 4 -9 -9 3 3 2 2 1 1 1 1 1 4 1 4 3 3 2 2 3 3 4 4 1 1
GT1 10 0 1 1 2 2 7 7 3 3 2 2 1 1 1 1 1 8 1 1 1 3 2 2 3 3 1 1 1 5
GT3 10 0 1 2 2 2 5 8 -9 -9 2 3 1 4 2 2 1 4 1 1 1 3 -9 -9 3 3 4 4 1 8
GT5 10 0 1 1 2 7 2 9 1 3 2 3 1 1 2 2 4 4 1 7 3 3 2 2 3 3 1 1 1 7
GT9 10 0 1 1 2 6 8 8 3 3 2 3 1 4 1 2 1 4 1 8 1 3 2 2 3 3 4 4 1 1
MX13 11 0 1 1 2 2 2 2 1 1 2 3 1 7 1 2 1 1 1 1 3 3 2 2 -9 -9 1 4 1 1
MX1 11 0 1 1 2 2 -9 -9 1 1 3 3 1 4 2 2 1 1 1 1 3 3 2 2 -9 -9 1 1 1 1
MX25 11 0 1 1 2 2 2 2 1 1 2 3 1 1 2 2 -9 -9 1 1 3 3 1 2 3 3 1 1 1 1
MX29 11 0 1 1 2 5 5 5 1 1 3 3 1 3 2 2 -9 -9 1 1 3 3 1 2 1 3 1 1 -9 -9
MX2 11 0 1 1 -9 -9 2 2 1 1 3 3 1 1 2 2 1 5 1 1 3 5 2 2 3 3 1 4 1 1
MX33 11 0 1 1 2 2 5 5 1 11 -9 -9 1 4 2 2 1 1 1 1 3 3 2 2 3 3 4 4 1 1
MX5 11 0 1 1 2 2 2 2 1 1 2 2 1 4 2 2 1 1 1 1 -9 -9 1 1 -9 -9 1 1 1 1
MX9 11 0 1 1 2 2 2 5 -9 -9 2 2 1 1 2 2 1 1 1 1 3 3 2 2 3 3 1 1 1 1
FT11 12 0 1 1 2 2 5 7 1 9 2 3 1 8 2 2 1 4 1 1 3 3 2 2 3 3 1 3 1 2
FT13 12 0 1 1 2 3 -9 -9 1 3 2 3 1 1 2 2 4 6 1 1 3 3 2 2 3 3 1 1 1 1
FT16 12 0 1 1 2 8 -9 -9 1 1 2 4 1 5 1 2 1 8 1 1 3 6 2 2 3 3 3 3 1 1
FT20 12 0 1 1 2 2 -9 -9 1 1 2 2 1 1 2 2 1 4 1 1 3 3 2 2 3 3 1 5 1 1
FT21 12 0 1 1 2 2 2 8 1 6 2 5 -9 -9 2 2 1 1 1 1 3 3 2 2 3 3 -9 -9 1 2
FT3 12 0 1 1 2 2 5 5 1 1 2 5 1 2 1 2 -9 -9 1 1 3 6 2 2 3 3 1 3 -9 -9
FT5 12 0 1 1 2 2 5 5 1 2 2 3 1 1 2 2 1 4 1 1 3 3 2 2 1 3 1 4 1 1
FT9 12 0 1 1 2 2 2 7 1 1 -9 -9 1 3 2 2 1 4 1 1 3 3 2 2 3 3 4 5 1 1
GS13 13 0 1 1 2 2 2 2 1 1 2 3 1 1 2 2 1 6 1 1 3 3 2 2 3 3 1 3 1 1
GS1 13 0 1 1 2 2 -9 -9 1 5 3 3 1 1 2 2 6 6 1 3 3 3 1 1 3 3 1 3 1 3
GS25 13 0 1 1 2 2 2 2 -9 -9 2 2 1 1 2 2 1 6 1 1 1 3 2 2 3 3 1 3 1 1
GS27 13 0 1 1 2 10 2 2 1 3 2 3 1 6 2 2 1 1 1 1 3 3 2 2 3 3 1 3 1 10
GS28 13 0 1 1 2 2 2 2 1 10 3 3 1 1 2 2 1 1 1 1 3 3 2 2 3 3 1 2 1 1
GS2 13 0 1 1 -9 -9 -9 -9 1 1 2 3 1 1 2 2 1 4 1 1 3 3 2 2 3 3 3 3 -9 -9
GS3 13 0 1 1 -9 -9 -9 -9 1 1 2 3 1 1 1 2 -9 -9 1 1 3 3 -9 -9 3 3 -9 -9 1 4
GS9 13 0 1 1 2 2 2 2 1 1 2 2 1 1 2 2 4 4 1 1 3 3 2 2 1 3 1 2 1 1


      Thank you,

      Ye






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