Search
Question: seqnames versus chrom
0
gravatar for felix.ernst
5 days 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 days ago by Michael Lawrence9.8k • written 5 days ago by felix.ernst0
1
gravatar for Michael Lawrence
5 days ago by
United States
Michael Lawrence9.8k wrote:

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

ADD COMMENTlink written 5 days ago by Michael Lawrence9.8k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 408 users visited in the last hour