Question: vcfR package vector length error
0
gravatar for jenniewoo
2.9 years ago by
jenniewoo20
United States
jenniewoo20 wrote:

I am trying to use vcfR package to do some plots but could not import hg19 reference genome fasta file. The error is 

long vectors not supported yet: ../../src/include/Rinlinedfuns.h:137

Any idea how to increase the vector length so that big fasta can be imported? Thanks.

>ape::read.dna(dna_file, format = "fasta", skip = 0,nlines = 0, comment.char = "#",as.character = FALSE, as.matrix = NULL)

> sessionInfo()
R version 3.2.3 (2015-12-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS release 6.8 (Final)

locale:
 [1] LC_CTYPE=en_US.iso885915       LC_NUMERIC=C                  
 [3] LC_TIME=en_US.iso885915        LC_COLLATE=en_US.iso885915    
 [5] LC_MONETARY=en_US.iso885915    LC_MESSAGES=en_US.iso885915   
 [7] LC_PAPER=en_US.iso885915       LC_NAME=C                     
 [9] LC_ADDRESS=C                   LC_TELEPHONE=C                
[11] LC_MEASUREMENT=en_US.iso885915 LC_IDENTIFICATION=C           

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

other attached packages:
[1] Rcpp_0.12.7          vcfR_1.2.0           BiocInstaller_1.20.3

loaded via a namespace (and not attached):
[1] magrittr_1.5      tools_3.2.3       nlme_3.1-128      ape_3.5          
[5] memuse_3.0-1      grid_3.2.3        pinfsc50_1.0.0    viridisLite_0.1.3
[9] lattice_0.20-34  

vcf • 568 views
ADD COMMENTlink modified 2.9 years ago by Martin Morgan ♦♦ 23k • written 2.9 years ago by jenniewoo20
Answer: vcfR package vector length error
0
gravatar for Martin Morgan
2.9 years ago by
Martin Morgan ♦♦ 23k
United States
Martin Morgan ♦♦ 23k wrote:

vcfR is a CRAN package, not a Bioconductor package. You'll need to contact maintainer("vcfR") or use VariantAnnotation. It looks like the problem is with the ape package, which is also a CRAN package; you could try to read the fasta file with Biostrings (that would be useful with VariantAnnotation, but not with vcfR).

ADD COMMENTlink modified 2.9 years ago • written 2.9 years ago by Martin Morgan ♦♦ 23k
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