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Question: seqnames versus chrom
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gravatar for felix.ernst
5 months 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.

Cheers,

Felix

 

 

ADD COMMENTlink modified 5 months ago by Michael Lawrence10.0k • written 5 months ago by felix.ernst0
1
gravatar for Michael Lawrence
5 months ago by
Michael Lawrence10.0k
United States
Michael Lawrence10.0k wrote:

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

ADD COMMENTlink written 5 months ago by Michael Lawrence10.0k
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