[BioC] good news and bad news
hpages at fhcrc.org
Thu Aug 16 19:16:13 CEST 2012
People generally ask "do you want me to start with the good or with
the bad news?" Here they are in no particular order (both are changes
in BioC devel):
- I've added the mcols() accessor as the preferred way (over
elementMetadata() and values()) to access the metadata columns.
Also the term "metadata columns" is now used consistently
everywhere in the IRanges/GenomicRanges/Rsamtools documentation
(instead of "element metadata", "elementMetadata columns",
"values", "columns of values", "metadata values",
"elementMetadata values", etc...)
Having 3 synonyms for accessing the same thing is of course not
ideal but I hope we can remedy this in the future.
- I've added "$" and "$<-" methods for GRanges *only*. Provided
as a convenience and as the result of strong popular demand. Note
that those methods are not consistent with the other "$" and "$<-"
methods defined in the IRanges/GenomicRanges infrastructure, and
might confuse some users by making them believe that a GRanges
object can be manipulated as a data.frame-like object. It is
therefore recommended to use them only interactively, and
their use in scripts or packages is discouraged (in that
case, 'mcols(x)$name' should be used instead of 'x$name').
Those changes are in IRanges 1.15.35 and GenomicRanges 1.9.48.
Please let me know if you have any questions or concerns about this.
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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