trouble with predictCoding( function
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@vakulmohanty-8232
Last seen 5.4 years ago
United States

I'm attempting to annotate SNPs from VCF files I have downloaded from the TCGA dataportal. I'm able to identify their locations, but when i try to use the predictCoding() "coding <- predictCoding(vcf,txdb,seqSource = Hsapiens)" to identify effect of the variants in the coding regions I get the following error

 Error in .getOneSeqFromBSgenomeMultipleSequences(x, names[i], start[i],  : 
  sequence ^1$ not found

Could someone suggest a work around or a way to fix the error. 

the version of R i use is version.string R version 3.2.0 (2015-04-16), in case that makes a difference.

Thank you, 

> version 


 

snp variantannotation predict coding • 921 views
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Hi,

Please show your sessionInfo().  What are txdb and Hsapiens? How did you get them? I suspect the problem is that the objects you supply to the vcf, txdb, and seqSource arguments don't use the same chromosome naming conventions.

H.

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