Issue with gl.impute() Function in dartR

[Jean Rodrigue Sangaré]

Hello everyone,
I’d like to share an error I encountered while trying to impute missing SNP data in a genlight object using the gl.impute() function.

Here’s what I tried:

gl_imputed <- gl.impute(gl, method = "mean") Starting gl.impute Processing genlight object with SNP data

Error in gl.impute(gl, method = "mean") : object 'x3' not found

> gl_imputed <- gl.impute(gl, method = "mode") Starting gl.impute Processing genlight object with SNP data

Error in gl.impute(gl, method = "mode") : object 'x3' not found

[Kndalem Yaregal]

Can I filter LD in geneligh object

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Thank you!

Kind regards,

Kndalem Yaregal 

MSc. Student in Plant Breeding and Genetics |Wollo University 

Plant Breeder |Sekota Dryland Agricultural Research Center  in Amhara Agricultural Research Institute 

Email (Alt): 21ethi...@gmail.com 

skype: Kndalem. Yaregal

 Mobile: +251916899864, Ethiopia

"Improving the Dryland for Mind Glad."

 "Make a positive impact in our community!"

[Jose Luis Mijangos]

Hi,

Thanks a lot for reporting this bug! Just to clarify, the function should run without issues as long as one of the four valid options is used for the method parameter: "frequency", "HW", "neighbour", or "random".

Cheers,
Luis

[Jose Luis Mijangos]

Hi

Please see some example code below that shows how you can filter on LD in a genlight object.

Cheers,
Luis

library(dartRverse)

# sample dataset
t1 <- platypus.gl

# Optional: if SNPs are mapped to a reference genome,
# assign SNP position and chromosome
t1$position <- t1$other$loc.metrics$ChromPos_Platypus_Chrom_NCBIv1
t1$chromosome <- as.factor(t1$other$loc.metrics$Chrom_Platypus_Chrom_NCBIv1)

# access function documentation
?gl.report.ld.map
# or
help(gl.report.ld.map)

# generate LD report
ld_res <- gl.report.ld.map(t1,
                           ld.max.pairwise = 10000000)

# filter on LD
t2 <- gl.filter.ld(t1,
                   ld.report = ld_res,
                   threshold = 0.2)