[adegenet-forum] unable to import a diploid dataset using read.strucutre
Jombart, Thibaut
t.jombart at imperial.ac.uk
Mon Jan 6 15:29:03 CET 2014
Hello,
this file looks wrong to me:
Individual labels (1 column) + population indication (1 column) + 14 markers (2 columns each = 28 columns) = 30 columns in total.
The best thing to do probably is to re-export your data using a different format (e.g. GENETIX, .gtx format), or manually merge the columns of the same markers together and use read.table and df2genind.
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: 01 January 2014 01:57
To: adegenet-forum at lists.r-forge.r-project.org
Subject: Re: [adegenet-forum] unable to import a diploid dataset using read.strucutre
Dear Thibaut
The file (31 columns) is a Structure format file obtained from Genalex. I try to read. structure by
obj <- read.structure(system.file("files/14loci.stru",package="adegenet"),n.ind=104,n.loc=14,onerowperind=TRUE,col.lab=1,col.pop=2,col.others=3,row.marknames=1,NA.char="-9")
and 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
If I remove the third column (pop flag), and read.structure by
obj <- read.structure(system.file("files/14loci.stru",package="adegenet"),n.ind=104,n.loc=14,onerowperind=TRUE,col.lab=1,col.pop=2,row.marknames=1,NA.char="-9")
The data cannot be imported and will be asked
Which other optional columns should be read (press 'return' when done)?
Can you help fix this? Thank you!
Ye
> -----原始邮件-----
> 发件人: "Jombart, Thibaut" <t.jombart at imperial.ac.uk<mailto:t.jombart at imperial.ac.uk>>
> 发送时间: 2013年12月30日 星期一
> 收件人: "sun-ye at scib.ac.cn<mailto:sun-ye at scib.ac.cn>" <sun-ye at scib.ac.cn<mailto:sun-ye at scib.ac.cn>>, "adegenet-forum at lists.r-forge.r-project.org<mailto:adegenet-forum at lists.r-forge.r-project.org>" <adegenet-forum at lists.r-forge.r-project.org<mailto:adegenet-forum at lists.r-forge.r-project.org>>
> 抄送:
> 主题: RE: [adegenet-forum] unable to import a diploid dataset using read.strucutre
>
> 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<mailto:adegenet-forum-bounces at lists.r-forge.r-project.org> [adegenet-forum-bounces at lists.r-forge.r-project.org<mailto:adegenet-forum-bounces at lists.r-forge.r-project.org>] on behalf of sun-ye at scib.ac.cn<mailto:sun-ye at scib.ac.cn> [sun-ye at scib.ac.cn<mailto:sun-ye at scib.ac.cn>]
> Sent: 30 December 2013 03:09
> To: adegenet-forum at lists.r-forge.r-project.org<mailto: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
>
>
>
>
--
Dr. Ye SUN
Key Laboratory of Plant Resources Conservation and Sustainable Utilization
South China Botanical Garden, Chinese Academy of Sciences
Xingke Road 723,Tianhe District, Guangzhou 510650, PR China
--
Dr. Ye SUN
Key Laboratory of Plant Resources Conservation and Sustainable Utilization
South China Botanical Garden, Chinese Academy of Sciences
Xingke Road 723,Tianhe District, Guangzhou 510650, PR China
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