`snp_autoSVD()` only works after a `library("bigsnpr")` call

[dramanica]

If using bigsnpr::snp_autoSVD() without first calling library("bigsnpr"), we get:

 object 'LD.wiki34' not found

This stems from line 119 in autoSVD.R, which is:

LRLDR <- LD.wiki34[0, 1:3]

Lazy loading does not happen in the function without previously loading the package. As the dataset is only used to initialise an empty data.frame, it would be better to simply use:

LRLDR <- data.frame(Chr=integer(), Start = integer(), Stop = integer())

so that the function can be used without the need to invoke library() first. Happy to create a pull request if it helps.

[privefl]

Thanks for reporting.

To reproduce:

bigsnp <- bigsnpr::snp_attachExtdata()
G <- bigsnp$genotypes
obj.svd <- bigsnpr::snp_autoSVD(G, bigsnp$map$chromosome)

• Maybe replacing by bigsnpr::LD.wiki34 would work as well.
• The same problem would appear for bed_autoSVD().

Do you want to submit a PR?

[dramanica]

Sure, happy to make a PR. Two quick question: 1) Do you want a unit test? 2) Do you have a preference for bigsnpr::LD.wiki34 vs explicitely creating an empty data.frame?

[privefl]

Your way is probably more direct/explicit.

I am not sure we can have a unit test about this. Maybe can unload the package before testing the function? Anyway, we won't test this for the other functions. So, we can drop the unit test if you want.

[dramanica]

Ok, happy to go with the lazy option of no unit test, especially as, when creating the data.frame from scratch, the unit test does not make that much sense any more. PR submitted.