Hi all, 

The rsidsToGRanges function gave the error message in SNPlocs.Hsapiens.dbSNP.20111119 library(dbSNP135) as follows:

library(SNPlocs.Hsapiens.dbSNP.20111119 )

rsidsToGRanges("rs6065094")

Error in get(name, envir = asNamespace(pkg), inherits = FALSE):

object 'anyMissing' not found. 

But rsidsToGRanges function using dbSNP137 or later version doesn't have any problem.

#########################################################

> sessionInfo()
R version 3.2.0 (2015-04-16)
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
[1] SNPlocs.Hsapiens.dbSNP.20111119_0.99.6
[2] GenomicRanges_1.20.5                  
[3] GenomeInfoDb_1.4.1                    
[4] IRanges_2.2.5                         
[5] S4Vectors_0.6.3                       
[6] BiocGenerics_0.14.0                   

loaded via a namespace (and not attached):
[1] XVector_0.8.0

#########################################################

Many thanks for any comment!

Best regards,

genefan

Hi genefan,

Thanks for the report. This should be fixed in SNPlocs.Hsapiens.dbSNP.20111119 version 0.99.7 which should become available thru biocLite() in the next couple of hours.

Please note that SNPlocs.Hsapiens.dbSNP.20111119 contains outdated dbSNP data (Build 135, from 2011). It's highly recommended that you use a SNPlocs package based on a more recent dbSNP build instead. See available.SNPs() for the list of SNPlocs packages currently available and make sure to pick up the most recent one (SNPlocs.Hsapiens.dbSNP144.GRCh37 and SNPlocs.Hsapiens.dbSNP144.GRCh38 at the moment).

Also please note that, starting with dbSNP Build 141, the naming scheme of the SNPlocs package has changed and there is a new API for extracting SNPs. The new API consists of 3 functions (snpsBySeqname(), snpsByOverlaps(), snpsById()) and is more flexible than the old API. See ?SNPlocs for more information.

Cheers,

H.

Hi Herve, 

thanks so much for your time and your suggestion. I just have to use the old version for my own purpose. The new API sounds great!

with the best,

genefan