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error in pi_around_gene in caroline.r #1

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rachelss opened this issue Oct 15, 2015 · 1 comment
Open

error in pi_around_gene in caroline.r #1

rachelss opened this issue Oct 15, 2015 · 1 comment
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@dwinter

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@rachelss
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when length(snp_ids) > 1000

Error in as.vector(x, "character") :
cannot coerce type 'externalptr' to vector of type 'character'
dwinter added a commit that referenced this issue Oct 16, 2015
@dwinter
Smaller 'chunk' size for pi_around_gene #1
05a5fda 
`pi_around_gene` now fetches SNPs in batches of 500.
Previously this was 1000 (the upper limit enforced by ensembl),
but this lead to occasional "drop outs".
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dwinter commented Oct 16, 2015

The "chunk size" is now 500, which seems to work.

We could probably re-factor the function to have some sort of counter when it's making multiple requests, because it takes a while to fetch them.

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