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

[Peng Yu]

I see. So we have the same version of oligo installed. But my document
for oligo is less than yours. Can somebody help me on this issue?

Regards,
Peng

On Thu, Aug 20, 2009 at 6:56 PM, Benilton Carvalho<bcarvalh at jhsph.edu> wrote:
> 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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>
>