Question: seqnames versus chrom
gravatar for felix.ernst
10 weeks ago by
felix.ernst0 wrote:

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.





ADD COMMENTlink modified 10 weeks ago by Michael Lawrence9.9k • written 10 weeks ago by felix.ernst0
gravatar for Michael Lawrence
10 weeks ago by
United States
Michael Lawrence9.9k wrote:

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

ADD COMMENTlink written 10 weeks ago by Michael Lawrence9.9k
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