Sometimes the following function call causes a database exception:> gene.seq <- getSequence (id=gene.map[,"ensembl_transcript_id"], type="ensembl_transcript_id",+ seqType="3utr", mart=hmart) I understand the above function must be called by try to capture the eventual error. WHat is not clear to me is how to realize that an error has occurred. The on-line documentation mentions an invisible object of class "try-error". How shall I test whetehr such object has been created or not ? I assume it is created whenever an error does occur ....? Thank you for your help. Maura tutti i telefonini TIM! [[alternative HTML version deleted]]
Hi, On Aug 3, 2009, at 11:53 AM, <mauede at alice.it> wrote:> Sometimes the following function call causes a database exception: > >> gene.seq <- getSequence (id=gene.map[,"ensembl_transcript_id"], >> type="ensembl_transcript_id", > + seqType="3utr", mart=hmart) > > I understand the above function must be called by try to capture the > eventual error. > WHat is not clear to me is how to realize that an error has > occurred. The on-line documentation > mentions an invisible object of class "try-error". > How shall I test whetehr such object has been created or not ? > I assume it is created whenever an error does occur ....?By "invisible" object, the documentation is saying that it's returning an object via the "invisible" function (see ?invisible). The object is no longer invisible if the function is called and the return value is assigned to a variable: which you are doing in your case. In your case, you just have to check to see if the object returned by getSequence is a (or inherits from) the "try-error" class. The last line of the help in ?try actually shows you how to do that. Here's a simpler example: R> m <- matrix(1:100, 10, 10) R> a <- try(m[,5]) # no error R> a [1] 41 42 43 44 45 46 47 48 49 50 R> b <- try(m[,11]) # error here b [1] "Error in try(m[, 11]) : subscript out of bounds\n" attr(,"class") To programmatically test if b is an error: R> is(b, 'try-error') [1] TRUE R> > inherits(b, 'try-error') # used in last line of ?try [1] TRUE -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact
gotError <- try(gene.seq <- getSequence
(id=gene.map[,"ensembl_transcript_id"],
type="ensembl_transcript_id",
seqType="3utr", mart=hmart))
if (inherits(gotError, 'try-error')){.....error occurred, do
recovery........}
On Mon, Aug 3, 2009 at 11:53 AM, <mauede at alice.it>
wrote:> Sometimes the following function call causes a database exception:
>
>> ?gene.seq <- getSequence
(id=gene.map[,"ensembl_transcript_id"],
type="ensembl_transcript_id",
> + ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?seqType="3utr", mart=hmart)
>
> I understand the above function must be called by try to capture the
eventual error.
> WHat is not clear to me is how to realize that an error has occurred. The
on-line documentation
> mentions an invisible object of class "try-error".
> How shall I test whetehr such object has been created or not ?
> I assume it is created whenever an error does occur ....?
>
> Thank you for your help.
> Maura
>
>
> tutti i telefonini TIM!
>
>
> ? ? ? ?[[alternative HTML version deleted]]
>
> ______________________________________________
> R-help at 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.
>
--
Jim Holtman
Cincinnati, OH
+1 513 646 9390
What is the problem that you are trying to solve?
Put your function in try() and the test it's class
gene.seq <- try(getSequence (id=gene.map[,"ensembl_transcript_id"],
type="ensembl_transcript_id", seqType="3utr", mart=hmart))
if(class(gene.seq) == "try-error"){
#code to run when an error occurs
} else {
#code to run when no error occurs
}
HTH,
Thierry
------------------------------------------------------------------------
----
ir. Thierry Onkelinx
Instituut voor natuur- en bosonderzoek / Research Institute for Nature
and Forest
Cel biometrie, methodologie en kwaliteitszorg / Section biometrics,
methodology and quality assurance
Gaverstraat 4
9500 Geraardsbergen
Belgium
tel. + 32 54/436 185
Thierry.Onkelinx at inbo.be
www.inbo.be
To call in the statistician after the experiment is done may be no more
than asking him to perform a post-mortem examination: he may be able to
say what the experiment died of.
~ Sir Ronald Aylmer Fisher
The plural of anecdote is not data.
~ Roger Brinner
The combination of some data and an aching desire for an answer does not
ensure that a reasonable answer can be extracted from a given body of
data.
~ John Tukey
-----Oorspronkelijk bericht-----
Van: r-help-bounces at r-project.org [mailto:r-help-bounces at r-project.org]
Namens mauede at alice.it
Verzonden: maandag 3 augustus 2009 17:54
Aan: r-help at stat.math.ethz.ch
Onderwerp: [R] How to catch an error using try
Sometimes the following function call causes a database exception:
> gene.seq <- getSequence
(id=gene.map[,"ensembl_transcript_id"],
> type="ensembl_transcript_id",
+ seqType="3utr", mart=hmart)
I understand the above function must be called by try to capture the
eventual error.
WHat is not clear to me is how to realize that an error has occurred.
The on-line documentation mentions an invisible object of class
"try-error".
How shall I test whetehr such object has been created or not ?
I assume it is created whenever an error does occur ....?
Thank you for your help.
Maura
tutti i telefonini TIM!
[[alternative HTML version deleted]]
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