seqnames versus chrom
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@felixernst-13698
Last seen 19 months ago

Dear all,

I can retrieve the chromosome names stored in a GRanges object either using GenomeInfoDb::seqnames() or rtracklayer::chrom(). This deviates from the use of the other accessor functions, such as BiocGenerics::start(), BiocGenerics::end(), etc

Is there a reason for this split up? Is there a best practice, which function (seqnames or chrom) to use?

Thanks for the suggestions.

Cheers,

Felix

 

 

BiocGen rtracklayer genomeinfodb • 511 views
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@michael-lawrence-3846
Last seen 7 weeks ago
United States

Stick with seqnames(). The chrom() accessor is from before GRanges existed. Should probably be deprecated.

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