[BioC] How to get the relative path with list.celfiles() from the oligo package?

[Benilton Carvalho]

Hi Peng,

That's not what I meant. My point was that my oligo version is the  
same as yours. Therefore, the documentation must be the same. And mine  
describes the use of "..." (dots).

b

On Aug 20, 2009, at 8:43 PM, Peng Yu wrote:

> Hi,
>
> So in summary, you use an older version of R than mine, but you get a
> newer version of help page. This is really strange. Can somebody help
> me figure out what the problem is with my R installation?
>
> Regards,
> Peng
>
> On Thu, Aug 20, 2009 at 4:51 PM, Benilton  
> Carvalho<bcarvalh at jhsph.edu> wrote:
>> Peng,
>>
>> the part that was omitted in your message was:
>>
>> Arguments:
>>
>>    ...: parameters to be passed to 'list.files'
>>
>> and note my sessionInfo() (it's a very old R 2.9.x that I'm  
>> running, but it
>> doesn't play a role in this case).
>>
>> b
>>
>>> sessionInfo()
>> R version 2.9.0 RC (2009-04-10 r48321)
>> x86_64-unknown-linux-gnu
>>
>> locale:
>> LC_CTYPE 
>> = 
>> en_US 
>> .iso885915 
>> ;LC_NUMERIC 
>> = 
>> C 
>> ;LC_TIME 
>> = 
>> en_US 
>> .iso885915 
>> ;LC_COLLATE 
>> = 
>> en_US 
>> .iso885915 
>> ;LC_MONETARY 
>> = 
>> C 
>> ;LC_MESSAGES 
>> = 
>> en_US 
>> .iso885915 
>> ;LC_PAPER 
>> = 
>> en_US 
>> .iso885915 
>> ;LC_NAME 
>> = 
>> C 
>> ;LC_ADDRESS 
>> =C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.iso885915;LC_IDENTIFICATION=C
>>
>> attached base packages:
>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>
>> other attached packages:
>> [1] oligo_1.8.1          preprocessCore_1.6.0 oligoClasses_1.6.0
>> [4] Biobase_2.4.1
>>
>> loaded via a namespace (and not attached):
>> [1] affxparser_1.17.2  affyio_1.12.0      Biostrings_2.11.52  
>> DBI_0.2-4
>> [5] IRanges_1.1.66     splines_2.9.0
>>
>>
>> On Aug 20, 2009, at 6:10 PM, Peng Yu wrote:
>>
>>> On Thu, Aug 20, 2009 at 3:31 PM, Sean Davis<seandavi at gmail.com>  
>>> wrote:
>>>>
>>>>
>>>> On Thu, Aug 20, 2009 at 4:24 PM, Peng Yu <pengyu.ut at gmail.com>  
>>>> wrote:
>>>>>
>>>>> Hi,
>>>>>
>>>>> I run the following command. But it only gives the file names. I  
>>>>> am
>>>>> wondering if there is a way to get the filename along with the
>>>>> directory name, i.e., 'data/ki10923.CEL', etc.
>>>>>
>>>>> Regards,
>>>>> Peng
>>>>>
>>>>>> list.celfiles('data/')
>>>>>
>>>>> [1] "ki10923.CEL" "ki10924.CEL" "ki10925.CEL" "ki10926.CEL"
>>>>> "ki10928.CEL"
>>>>> [6] "wt10921.CEL" "wt10922.CEL" "wt10927.CEL" "wt10930.CEL"
>>>>> "wt10980.CEL"
>>>>
>>>> Hi, Peng.
>>>>
>>>> Reading the help for list.celfiles(), it suggests that all  
>>>> arguments are
>>>> passed along to the list.files().  Reading the help for  
>>>> list.files()
>>>> suggests that including full.names=TRUE will return the  
>>>> information you
>>>> want.
>>>>
>>>> Sean
>>>>
>>>>
>>>
>>> I have checked the help page before I sent the message. But the help
>>> page that I got did not show much information. See below the  
>>> email. My
>>> sessionInfo is shown below the help page. Is my documentation
>>> outdated? I remember that my R installation was updated only two  
>>> weeks
>>> ago.
>>>
>>> Regards,
>>> Peng
>>>
>>> list.celfiles             package:oligo             R Documentation
>>>
>>> List CEL/XYS files
>>>
>>> Description:
>>>
>>>   Lists the CEL/XYS files.
>>>
>>> Usage:
>>>
>>>   list.celfiles(...)
>>>
>>> Arguments:
>>>
>>>
>>>
>>> Value:
>>>
>>>   Character vector with the filenames.
>>>
>>> Examples:
>>>
>>>   list.xysfiles()
>>>   list.celfiles()
>>>
>>>
>>>
>>>> sessionInfo()
>>>
>>> R version 2.9.1 (2009-06-26)
>>> x86_64-unknown-linux-gnu
>>>
>>> locale:
>>>
>>> LC_CTYPE 
>>> = 
>>> en_US 
>>> .UTF 
>>> -8 
>>> ;LC_NUMERIC 
>>> = 
>>> C 
>>> ;LC_TIME 
>>> = 
>>> en_US 
>>> .UTF 
>>> -8 
>>> ;LC_COLLATE 
>>> = 
>>> en_US 
>>> .UTF 
>>> -8 
>>> ;LC_MONETARY 
>>> = 
>>> C 
>>> ;LC_MESSAGES 
>>> = 
>>> en_US 
>>> .UTF 
>>> -8 
>>> ;LC_PAPER 
>>> = 
>>> en_US 
>>> .UTF 
>>> -8 
>>> ;LC_NAME 
>>> = 
>>> C 
>>> ;LC_ADDRESS 
>>> =C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
>>>
>>> attached base packages:
>>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>>
>>> other attached packages:
>>> [1] oligo_1.8.1          preprocessCore_1.6.0 oligoClasses_1.6.0
>>> [4] Biobase_2.4.1
>>>
>>> loaded via a namespace (and not attached):
>>> [1] affxparser_1.16.0 affyio_1.12.0     Biostrings_2.12.8 DBI_0.2-4
>>> [5] IRanges_1.2.3     splines_2.9.1
>>>
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>>
>>
>
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