[BioC] New SNPlocs data package for Human (dbSNP BUILD 131)

[Hervé Pagès]

Hi Lin,

Lin Tang wrote:
> Hi, Dear Hervé
> 
> Thanks so much for quickly assemble the new package. I have installed the hg19 and the new SNP packages, but I get error when try to "injectNSPs", do you have any clue what the problem might be? Thanks!
> 
> Regards,
> Lin
> 
>> library("BSgenome.Hsapiens.UCSC.hg19")
>> library("SNPlocs.Hsapiens.dbSNP.20100427")
>> HsWithSNPs = injectSNPs(Hsapiens, "SNPlocs.Hsapiens.dbSNP.20100427")
> Error in injectSNPs(Hsapiens, "SNPlocs.Hsapiens.dbSNP.20100427") : 
>   sequence names in package SNPlocs.Hsapiens.dbSNP.20100427 are not compatible with those in genome 'x'

The injection mechanism has changed. Now it uses an internal (defined
in the SNPlocs package) to translate from UCSC chromosome names to
NCBI/dbSNP chromosome names. This new mechanism is implemented in
BSgenome 1.16.1. This is why, in my previous email, I wrote:

   Please make sure you update BSgenome to >= 1.16.1 (available in
   about 12 hours thru biocLite) before you try to inject those SNPs
   in BSgenome.Hsapiens.UCSC.hg19.

Cheers,
H.


>> Hsapiens
> Human genome
> | 
> | organism: Homo sapiens (Human)
> | provider: UCSC
> | provider version: hg19
> | release date: Feb. 2009
> | release name: Genome Reference Consortium GRCh37
> | 
> | single sequences (see '?seqnames'):
> |   chr1                   chr2                   chr3                   chr4                 
> |   chr5                   chr6                   chr7                   chr8                 
> |   chr9                   chr10                  chr11                  chr12                
> |   chr13                  chr14                  chr15                  chr16                
> |   chr17                  chr18                  chr19                  chr20                
> |   chr21                  chr22                  chrX                   chrY                 
> |   chrM                   chr1_gl000191_random   chr1_gl000192_random   chr4_ctg9_hap1       
> |   chr4_gl000193_random   chr4_gl000194_random   chr6_apd_hap1          chr6_cox_hap2        
> |   chr6_dbb_hap3          chr6_mann_hap4         chr6_mcf_hap5          chr6_qbl_hap6        
> |   chr6_ssto_hap7         chr7_gl000195_random   chr8_gl000196_random   chr8_gl000197_random 
> |   chr9_gl000198_random   chr9_gl000199_random   chr9_gl000200_random   chr9_gl000201_random 
> |   chr11_gl000202_random  chr17_ctg5_hap1        chr17_gl000203_random  chr17_gl000204_random
> |   chr17_gl000205_random  chr17_gl000206_random  chr18_gl000207_random  chr19_gl000208_random
> |   chr19_gl000209_random  chr21_gl000210_random  chrUn_gl000211         chrUn_gl000212       
> |   chrUn_gl000213         chrUn_gl000214         chrUn_gl000215         chrUn_gl000216       
> |   chrUn_gl000217         chrUn_gl000218         chrUn_gl000219         chrUn_gl000220       
> |   chrUn_gl000221         chrUn_gl000222         chrUn_gl000223         chrUn_gl000224       
> |   chrUn_gl000225         chrUn_gl000226         chrUn_gl000227         chrUn_gl000228       
> |   chrUn_gl000229         chrUn_gl000230         chrUn_gl000231         chrUn_gl000232       
> |   chrUn_gl000233         chrUn_gl000234         chrUn_gl000235         chrUn_gl000236       
> |   chrUn_gl000237         chrUn_gl000238         chrUn_gl000239         chrUn_gl000240       
> |   chrUn_gl000241         chrUn_gl000242         chrUn_gl000243         chrUn_gl000244       
> |   chrUn_gl000245         chrUn_gl000246         chrUn_gl000247         chrUn_gl000248       
> |   chrUn_gl000249         
> | 
> | multiple sequences (see '?mseqnames'):
> |   upstream1000  upstream2000  upstream5000  
> | 
> | (use the '$' or '[[' operator to access a given sequence)
> 
> 
> 
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-- 
Hervé Pagès

Program in Computational Biology
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