gl.filter.callrate error if monomorphs == FALSE?

[Caroline Chong]

Hi All,

Thanks for version 1.8.3 and also the added capability for silicoDArT data - extremely timely!

I have a question about running gl.filter.callrate using v. 1.8.3. on a SNP data set that does not contain monomorphs.

Using previous versions of dartR I can successfully run, for example,

gl7 <- gl.filter.callrate(glx, threshold = 0.95, v=5)

but in v. 1.8.3 I now get returned the error on the same input data glx:

Starting gl.filter.callrate [ Build = Jacob ]

  Processing a SNP dataset

Error in if (x@other$loc.metrics.flags$monomorphs == FALSE) { :

  argument is of length zero

- Would you have any suggestions on what might be the issue? The genlight object "glx" already does not contain any monomorphs:

gl.report.monomorphs(glx)

Starting gl.report.monomorphs

  Processing a SNP dataset

  Identifying monomorphic loci

 No. of loci: 51329

    Polymorphic loci: 51329

    Monomorphic loci: 0

    Loci scored all NA: 0

  No. of individuals: 509

  No. of populations: 11

Completed: gl.report.monomorphs

NULL

Thanks for your suggestions,

Best regards, Caroline.

Threatened Species Botanist, Northern Territory Government, Darwin.

[Arthur Georges]

Hi Caroline,

can you run

glx <- gl.compatability.check(glx)

and try again.

A

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[Caroline Chong]

Hi Arthur,

Brilliant, thanks. I ran gl.compliance.check (not gl.compatability.check), got returned the following, and then successfully ran gl.filter.callrate.

Thanks for your help! Are you able to hazard what the problem was - would this have been the locus metrics needing recalculation?

Best regards, Caroline.

glx <- gl.compliance.check(glx)

Starting gl.compliance.check

  Processing a SNP dataset

  Checking coding of SNPs

    SNP data scored NA, 0, 1 or 2 confirmed

  Checking locus metrics and flags

  Recalculating locus metrics

  Checking for monomorphic loci

    No monomorphic loci detected

  Checking for individual metrics

    Individual metrics confirmed

  Checking for population assignments

  Population assignments confirmed

Spelling of coordinates checked and changed if necessary

Completed: gl.compliance.check

[Arthur Georges]

gl objects created under previous versions of dartR need to be updated for use in version 1,8,3. 

A

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