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Simon-Coetzee / motifBreakR

A Package For Predicting The Disruptiveness Of Single Nucleotide Polymorphisms On Transcription Factor Binding Sites.
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snps.from.rsid error to load XtraSNPlocs.Hsapiens.dbSNP144.GRCh37 #15

Open xinyixinyijiang opened 5 years ago

xinyixinyijiang commented 5 years ago

Hi, I have two indels to investigate their function, which should be in XtraSNPlocs.Hsapiens.dbSNP144.GRCh37. This SNPlocus object should be available in snps.from.rsid function? since it is outputted by available.SNPs().

But I got error: 

Error in snps.from.rsid(rsid = indels, dbSNP = XtraSNPlocs.Hsapiens.dbSNP144.GRCh37,  : 
  dbSNP argument was not provided with a valid SNPlocs object.
Please run availible.SNPs() to check for availible SNPlocs

Here is my code:

snps.mb <- snps.from.rsid(rsid = indels,
                          dbSNP = XtraSNPlocs.Hsapiens.dbSNP144.GRCh37,
                          search.genome = BSgenome.Hsapiens.UCSC.hg19)

Here is my sessioninfo:

R version 3.5.0 (2018-04-23)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Scientific Linux 7.2 (Nitrogen)

Matrix products: default
BLAS: /gpfs/igmmfs01/software/pkg/el7/apps/R/3.5.0/lib64/R/lib/libRblas.so
LAPACK: /gpfs/igmmfs01/software/pkg/el7/apps/R/3.5.0/lib64/R/lib/libRlapack.so

locale:
 [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C               LC_TIME=en_GB.UTF-8       
 [4] LC_COLLATE=en_GB.UTF-8     LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_GB.UTF-8   
 [7] LC_PAPER=en_GB.UTF-8       LC_NAME=C                  LC_ADDRESS=C              
[10] LC_TELEPHONE=C             LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
 [1] SNPlocs.Hsapiens.dbSNP144.GRCh37_0.99.20     BSgenome.Hsapiens.UCSC.hg19_1.4.0           
 [3] XtraSNPlocs.Hsapiens.dbSNP144.GRCh37_0.99.12 BSgenome_1.50.0                             
 [5] rtracklayer_1.42.0                           GenomicRanges_1.34.0                        
 [7] GenomeInfoDb_1.18.0                          motifbreakR_1.12.0                          
 [9] MotifDb_1.24.1                               Biostrings_2.50.1                           
[11] XVector_0.22.0                               IRanges_2.16.0                              
[13] S4Vectors_0.20.1                             BiocGenerics_0.28.0

Thanks a lot! Best wishes.

Simon-Coetzee commented 5 years ago

Indels are not currently under the purview of motifbreakR, but an update currently in the works will support indels in addition to SNVs. I will keep you updated here.

xinyixinyijiang commented 5 years ago

Okay! Thank you very much and look forward to your update!