CustomProDB: specify a snp dataset to be used for the SNP annotation
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@c315f3e7
Last seen 29 days ago
Germany

Hi guys, I need to specify a SNP dataset to prepare the annotation data. I am unable to find a version that works. Could anyone please help with the selection of a working version.

Code

library(customProDB)

ensembl <- useMart(
  "ENSEMBL_MART_ENSEMBL",
  dataset="hsapiens_gene_ensembl",
  host="https://aug2017.archive.ensembl.org",
  path="/biomart/martservice",
  archive=FALSE
)

annotation_path <- "<your_path>"

PrepareAnnotationEnsembl(
  mart=ensembl,
  annotation_path=annotation_path,
  splice_matrix=FALSE,
  dbsnp='snpedia',
  COSMIC=FALSE
)

Output

Prepare gene/transcript/protein id mapping information (ids.RData) ...  done
Build TranscriptDB object (txdb.sqlite) ... 
Download and preprocess the 'transcripts' data frame ... OK
Download and preprocess the 'chrominfo' data frame ... OK
Download and preprocess the 'splicings' data frame ... OK
Download and preprocess the 'genes' data frame ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... OK
 done
Prepare exon annotation information (exon_anno.RData) ...  done
 done                                                                                                                  
 done                                                                                                               
Prepare dbSNP information (dbsnpinCoding.RData) ... Error in normArgTable(value, x) : 
  Table 'snpediaCodingDbSnp' is unavailable
In addition: Warning message:
Ensembl will soon enforce the use of https.
Ensure the 'host' argument includes "https://" 
customProDB • 62 views
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