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wenbostar / PGA

PGA: a tool for ProteoGenomics Analysis
http://wenbostar.github.io/PGA/
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functions to use in loading own data #15

Open Jokendo-collab opened 4 years ago

Jokendo-collab commented 4 years ago

Hi,

I have a problem loading the vcf,gtf and bed files using this package. Can there be a section in the readme file where users can be guided on how to run their own data apart from the example data which comes with the package? I desperately need your assistance in this. I have followed the procedure accordingly in the tutorial file and things don't work with my data.

Thanks, Javan

Jokendo-collab commented 4 years ago

This is the error: dbfile <- dbCreator(gtfFile=gtffile,vcfFile=vcffile,bedFile=bedfile,annotation_path=annotation,outfile_name=outfile_name,genome=Hsapiens,outdir=outfile_path) Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘scanVcf’ for signature ‘"vcfR", "missing"’ Calls: dbCreator -> InputVcf -> scanVcf -> Execution halted

Shawn-Xu commented 4 years ago

Could you please provide the sessionInfo（)? I guess it may be that your R or package version is too old.
I suggest you to re-install the latest version of R and the latest PGA package from bioconductor.