Error in gl2vcf

[Marcelo Rosas]

Hi dartR team, & Luis

with a genlight object created with dartR, I can generate reports, monomorphs, overshoot, reproducibility and callrate filters. I can save as rds and csv . But when I try to export to PLINK and save I get the error

 

Error in names(x) <- value :

  'names' attribute [2] must be the same length as the vector [1]  
 

the same error also occurs when trying to export as vcf with   gl2vcf

thanks

Marcelo Rosas

[Elspeth McLennan]

Hi Marcelo, 

I'm having the same problem when trying to convert gl2plink. Did you have any luck getting this one to work?

Thanks, 

Elle

[Jose Luis Mijangos]

Hi Elle,

I think this bug has been fixed and it is available in the beta version of dartR. You can installl this version as shown below:

> library(dartR)
> gl.install.vanilla.dartR(flavour = "dev”)

Than please try again to run the gl2plink function .

Cheers,
Luis

> On 17 Mar 2023, at 2:24 pm, Elspeth McLennan <elle.mc...@gmail.com> wrote:
>
> Elle

[Elspeth McLennan]

Hi Luis, 

That worked perfectly, thank you!

Cheers, 

Elle

[Elspeth McLennan]

Hi Luis, 

Unfortunately I've run into this problem again when trying to convert to a plink format - it works with another one of my datasets so I'm thinking it must be something I'm doing wrong or with my data. I have tried the following from another post but am getting the same result:

# assigning chromosome information
gl_drop$chromosome <- gl_drop$other$loc.metrics$Chrom_Tammar_Chrom_NCBIv1
# assigning position information
gl_drop$position <- test$other$loc.metrics$ChromPos_Tammar_Chrom_NCBIv1
# converting to bed file
gl2plink(gl_drop, outfile = "plink_pw", outpath = "./", bed_file = TRUE)

Then getting this error:

> gl2plink(gl_drop, outfile = "plink_pw", outpath = "./", bed_file = TRUE) Starting gl2plink Processing genlight object with SNP data Chromosome slot is empty. Using 1 as dummy name. Error in names(x) <- value : 'names' attribute [2] must be the same length as the vector [1]

It may be to do with how I'm trying to rename the chromosomes? I wasn't sure where your example came from with the platypus.

Happy to send over my gl_drop.Rdata file if you need.

Thank you for your help in advance!

Elle

[Jose Luis Mijangos]

Hi Elle,

Can you please try installing the developing version of dartR.base as shown below. Note the change in the name of the parameter "bed.files". Also, the plink executable should be in your working directory. Double click on your plink executable to make sure that it can be run without issues.

#installing the developing version of dartR.base

devtools::install_github("green-striped-gecko/dartR.base@dev")
library(dartRverse)
load("gl_drop.Rdata")

gl2plink(gl_drop,
         outfile = "plink_pw",
         outpath = "./",

         bed.files = TRUE)

Cheers,

Luis 

[Elspeth McLennan]

Hi Luis, 

That worked - thank you!

Elle

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