Error in gl.report.bases

[NURUL AFIA ABD. MAJID]

 I have filtered my SNP data and saved the result as f6.Rdata. I want to analyze the SNP types and display the results in a table similar to the example below. I used the following command but encountered an error.  Can you please help me resolve this issue?

> t1 <- readRDS("f6.Rdata") > gl.report.bases( + t1, + plot.out = TRUE, + plot_colors = two_colors, + save2tmp = FALSE, + verbose = NULL) Starting gl.report.bases Processing genlight object with SNP data Error in gl.report.bases(t1, plot.out = TRUE, plot_colors = two_colors, : Fatal Error: Dataset does not include variable TrimmedSequence!

[Jose Luis Mijangos]

Hi,

We are working with DArT to determine a way to consistently use the same name for the trimmed sequence. 

In the meantime, I would recommend creating the field "TrimmedSequence” using the “trimmedSequenceSNP” as shown below:

> your_gl$other$loc.metrics$TrimmedSequence <- your_gl$other$loc.metrics$TrimmedSequenceSnp

Cheers

Luis

[Arthur Georges]

Hi Luis,

Maybe we could modify the scripts that require trimmed sequences to check for "TrimmedSequence” and if it does not exist, to check for “trimmedSequenceSNP” before giving the error?

A

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