Message-ID: <b91ac001-1f42-1333-09a7-56a30d04988d@fredhutch.org>
Date: 2018-08-04T17:08:30Z
From: Hervé Pagès
Subject: [Bioc-devel] Special meta column name in GRanges cause invalid object
In-Reply-To: <-hbmla6-2ek5i4-39l3kf-obclrd-23j5mg-f52fjtxyprkt10nyuvjx699czdkf5zezaixz-6lwclk8y4fb1ralu9qmiizbhe309l0-qkp375-3rtcli-a9012g6oaa5wvbgyzv5gbw7vo7x7vs872kyn.1532564456646@email.android.com>
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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--
Herv? Pag?s
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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