Gviz: UcscTrack() getting error when there is no genes in the region
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shuoguo ▴ 10
@shuoguo-10625
Last seen 5.1 years ago

I have this function and sometimes it gives me error:

refGenes <- UcscTrack(track="RefSeq Genes",
                        table="refGene",
                        trackType="GeneRegionTrack",
                        genome=genome_build,
                        chromosome=chrom,
                        from=pos0, to=pos1,
                        rstart="exonStarts", rends="exonEnds",
                        gene="name",
                        symbol="name2",
                        transcript="name",
                        strand="strand",
                        name="RefSeq Genes",
                        feature="name2",
                        showId=T,
                        fill = "green")

Error in make.unique(rep(if (!missing(feature) && !is.null(feature)) as.character(feature) else covars[["feature"]],  :
  'names' must be a character vector

I wonder if it is due to the fact that there was no genes in the region. e.g.

​[1] "chr16"    "33379409" "33476447"
 

Any way to by passing this?

 

Thanks a lot,

 

Shuoguo

 

givz UcscTrack • 574 views
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1
Entering edit mode
shuoguo ▴ 10
@shuoguo-10625
Last seen 5.1 years ago

Just in case in the future people run into the same issue. 

I have temporarily "fixed" this issue by removing the two lines in the command:

gene="name",
feature="name2",

please let me know if you have other ways.

Thanks,

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