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

[Benilton Carvalho]

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 outdated?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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