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