Bioconductor / GenomeInfoDb

Utilities for manipulating chromosome names, including modifying them to follow a particular naming style
https://bioconductor.org/packages/GenomeInfoDb
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N-ary nature of merge,Seqinfo,Seqinfo-method is not documented. #19

Closed LTLA closed 3 years ago

LTLA commented 3 years ago

As briefly mentioned in Bioconductor/GenomicRanges#54. Currently, I only see in ?Seqinfo:

‘merge(x, y)’: Merge ‘x’ and ‘y’ into a single Seqinfo object where the
          keys (aka the seqnames) are ‘union(seqnames(x),
          seqnames(y))’.  If a row in ‘y’ has the same key as a row in
          ‘x’, and if the 2 rows contain compatible information (NA
          values are compatible with anything), then they are merged
          into a single row in the result.  If they cannot be merged
          (because they contain different seqlengths, and/or
          circularity flags, and/or genome identifiers), then an error
          is raised.  In addition to check for incompatible sequence
          information, ‘merge(x, y)’ also compares ‘seqnames(x)’ with
          ‘seqnames(y)’ and issues a warning if each of them has names
          not in the other. The purpose of these checks is to try to
          detect situations where the user might be combining or
          comparing objects based on different reference genomes.

A user could possibly infer the presence of N-ary functionality for Seqinfo's merge from ?"merge,Vector,Vector-method", if one happened to stumble across that documentation... but I wouldn't bet on it.

hpages commented 3 years ago

Taken care of in GenomeInfoDb 1.27.6.

Just to clarify, Seqinfo objects are not Vector derivatives so whatever ?"merge,Vector,Vector-method" says is unrelated to this.