Re: [R] Methods to explore R data structures
Great, these are valuable tips. Thanks both of you. I appreciate it. :) Timothy [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Methods to explore R data structures
Hi, I'm very confused about R structures and the methods to go with them. I'm using R for microarray analysis with Bioconductors. Suppose without reading the documentations, what's the best way to explore a data structure when you know nothing about it? I am currently using is() / class() to see what the object is. str() / attributes() to probe inside the object, and someth...@something$something to walk it and explore. Is there any other way? Also, without reading documentations, is there a way to know what functions are available to extract data from it? For example, there is sampleNames() which works on ExpressionSet and AnnotatedDataFrame (which is a part of ExpressionSet). How do I know they are available (as sometimes I can't recall where I've seen them and I forgot the function names). And what are R functions? Are those two separate functions or polymorphic functions? I'm also pretty confused about S3, S4, or the regular list. I guess I'm fairly confused about R in general. Any good source of reading (hopefully short and understandable, too) would be appreciated. Thanks. Timothy [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Methods to explore R data structures
On 05/27/2010 02:13 AM, Timothy Wu wrote:
Hi,
I'm very confused about R structures and the methods to go with them.
I'm using R for microarray analysis with Bioconductors. Suppose
without reading the documentations, what's the best way to explore a
data structure when you know nothing about it?
probably by reading the documentation, especially vignettes
browseVignettes(Biobase)
and then switching to your web browser. If you're asking about
Bioconductor functionality in particular, then the Bioconductor mailing
list is appropriate
http://bioconductor.org/docs/mailList.html
I am currently using is() / class() to see what the object is. str()
/ attributes() to probe inside the object, and
someth...@something$something to walk it and explore. Is there any
This looks at the structure, but many classes will want to be
manipulated by their API.
other way? . Also, without reading documentations, is there a way to
know what functions are available to extract data from it? For
example, there is sampleNames() which works on ExpressionSet and
AnnotatedDataFrame (which is a part of ExpressionSet). How do I know
they are available (as sometimes I can't recall where I've seen them
and I forgot the function names). And what are R functions? Are
those
For an S4 object 'x', I'd
class(x)
getClass(cls)@package
followed by
showMethods(classes='ExpressionSet',
where=getNamespace('Biobase'))
or
cls - c(class(x), getClass(class(x))@contains)
pkg - getClass(cls)@package
showMethods(classes=cls, where=getNamespace(pkg))
and conversely
showMethods(sampleNames, where=getNamespace(pkg))
Methods for S3 classes can be found in a similar way, but using
'methods'. Both of these only discover classes in packages that are
loaded in the currently active session. This will miss plain old
functions that don't declare what type of object they intend to operate
on. If whan you say 'what are the R functions' you're asking for the
function definition, then
selectMethod(sampleNames, 'ExpressionSet')
two separate functions or polymorphic functions? I'm also pretty
sampleNames is a generic. There are methods that operate on eSet (a base
class of ExpressionSet), and on AnnotatedDataFrame.
confused about S3, S4, or the regular list. I guess I'm fairly
confused about R in general.
For S4
?Methods
?Classes
For S3, maybe section 10.9 of RShowDoc('R-intro')
Martin
Any good source of reading (hopefully short and understandable, too)
would be appreciated. Thanks.
Timothy
[[alternative HTML version deleted]]
__ R-help@r-project.org
mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do
read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109
Location: Arnold Building M1 B861
Phone: (206) 667-2793
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Methods to explore R data structures
The TkListView function in the TeachingDemos package is an interactive tool for looking at the structure and contents of lists and other objects. -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare greg.s...@imail.org 801.408.8111 -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r- project.org] On Behalf Of Timothy Wu Sent: Thursday, May 27, 2010 3:14 AM To: r-help@r-project.org Subject: [R] Methods to explore R data structures Hi, I'm very confused about R structures and the methods to go with them. I'm using R for microarray analysis with Bioconductors. Suppose without reading the documentations, what's the best way to explore a data structure when you know nothing about it? I am currently using is() / class() to see what the object is. str() / attributes() to probe inside the object, and someth...@something$something to walk it and explore. Is there any other way? Also, without reading documentations, is there a way to know what functions are available to extract data from it? For example, there is sampleNames() which works on ExpressionSet and AnnotatedDataFrame (which is a part of ExpressionSet). How do I know they are available (as sometimes I can't recall where I've seen them and I forgot the function names). And what are R functions? Are those two separate functions or polymorphic functions? I'm also pretty confused about S3, S4, or the regular list. I guess I'm fairly confused about R in general. Any good source of reading (hopefully short and understandable, too) would be appreciated. Thanks. Timothy [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting- guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
