Question: Create VRanges object from mutation data (txt extracted from annotated vcf)
0
3.0 years ago by
University of Arizona
gaiusjaugustus0 wrote:

I am working on using the SomaticSignatures package on a list of mutations I've received from a collaborator.  The file has all the variants listed in a tab-delimited text file, with all the fields you would expect from an annotated vcf file (e.g. Chromosome, Start_Position, End_Position, Reference_Allele, Tumor_Seq_allele, etc) named "CCCC_muts"

In order to get this working, I'm trying to create a VRanges object from this text file.  I ran the following command to try to accomplish this:

mutations <- VRanges(
seqnames = seqnames(as.character(CCCC_muts$Chromosome)), ranges = ranges(CCCC_muts, start = CCCC_muts$Start_Position, end = CCCC_muts$End_Position), ref = CCCC_muts$Reference_Allele,
alt = CCCC_muts$Tumor_Seq_Allele2, sampleNames = CCCC_muts$Barcode
)

I'm getting an error:

Error in (function (classes, fdef, mtable)  :
unable to find an inherited method for function ‘ranges’ for signature ‘"X"’

(where X is whatever type of data I try to put into it)

Because I'm unsure how to create the proper ranges format from my CCCC_muts file, and perhaps because of some other reason I don't understand.  Any help in resolving this issue would be awesome.

variantannotation iranges • 531 views
modified 3.0 years ago by Michael Lawrence11k • written 3.0 years ago by gaiusjaugustus0

In order to fix this, I had to convert my original dataframe to a GRanges object.  Then I had to input some fields as GRanges objects and some from the original text file.

VRanges(
seqnames = seqnames(CCCC_GRanges),
ranges = ranges(CCCC_GRanges),
ref = CCCC_muts$Reference_Allele, alt = CCCC_muts$Tumor_Seq_Allele2,
sampleNames = CCCC_muts2\$Barcode
)

Answer: Create VRanges object from mutation data (txt extracted from annotated vcf)
0
3.0 years ago by
United States
Michael Lawrence11k wrote:

I think you want something like:

mutations <- with(CCCC_muts, VRanges(
seqnames = Chromosome,
ranges = IRanges(Start_Position, End_Position),
ref = Reference_Allele,
alt = Tumor_Seq_Allele2,
sampleNames = Barcode
))