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

[Peng Yu]

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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>
>