User: klmr

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Posts by klmr

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Comment: C: biomaRt crashes when result contains missing values
... “the attributes don't come back in the same order that you requested them.” — That’s a known bug, and according to personal communication from the Ensembl team, the authors of Ensembl Biomart and biomaRt cannot agree on whose fault this is, hence no fix. ...
written 3.4 years ago by klmr0
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Comment: C: biomaRt crashes when result contains missing values
... I find it hard to infer that this shouldn’t work merely from the HTML interface, since it’s not documented anywhere (neither in the official documentation, nor in Ensembl Biomart or ‹biomaRt›) whether restrictions apply. At any rate the query undeniably *works* and returns a result, ‹biomaRt› just f ...
written 3.4 years ago by klmr0
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biomaRt crashes when result contains missing values
... When trying to access certain attributes via ‹biomaRt›, I get an error which seems to indicate a faulty Biomart data transfer. Here’s an annotated MWE: library(biomaRt) ensembl = useMart('ensembl', 'celegans_gene_ensembl') attr = c('ensembl_gene_id', 'external_gene_name', 'entrezgene', 'coding') x ...
biomart bug written 3.4 years ago by klmr0 • updated 3.4 years ago by Mike Smith4.0k

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