[Bioc-devel] Special meta column name in GRanges cause invalid object

Hervé Pagès hp@ge@ @ending from fredhutch@org
Sat Aug 4 19:08:30 CEST 2018


Thanks Jialin for the report. This should be addressed in GenomicRanges
1.33.13:

 
https://github.com/Bioconductor/GenomicRanges/commit/9fa12796dcb076ddb34b6f2c8115e358d9a0aeab

Other "show" methods suffer from the same problem (e.g. methods for
IRanges, Hits, GAlignments, etc...) and will also need to be fixed.

Cheers,
H.

On 07/25/2018 05:20 PM, marlin- using gmx.cn wrote:
> Dear bioc-devel,
> 
> I am not sure whether I should bring this up. This is a problem that would happen only in some rare cases. When the name of a meta column of GRanges is the name of an argument in the data.frame function, such as stringsAsFactors, the GRanges will not able to print and some functions will not work.
> 
> For example,
> gr = GRanges('chr1', IRanges(1, 14))
> gr$stringsAsFactors = -42
> gr
> 
> I believe this is due to S4Vectors use do.call(data.frame) to pass columns and some arguments to data.frame by joining them together as a list.
> 
> 
> Best,
> Jialin
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-- 
Hervé Pagès

Program in Computational Biology
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