[BioC] (no subject)

[James W. MacDonald]

Hi Qing,

Qing Jing wrote:
> 
> 
> 
> 
> 
> Dear List£¬
> 
> 
>  
> 
> I am a beginner in learning the package of
> Biostrings currently and for practice doing an example.
> 
> 
>  
> 
>  library(Biostrings);
>  dnaAlph<-new("BioPatternAlphabet",DNAAlphabet(),c(N="AGCT",
>  B="CGT",D="AGT",H="ACT",K="GT",M="AC",R="AG",S="CG",
>  V="ACG",W="AT",Y="CT"));
> Error in getClass(Class, where =
> topenv(parent.frame())) : 
>        
> "BioPatternAlphabet" is not a defined
> class

The Biostrings package has been refactored quite a bit, and no longer 
uses this class (a Google for 'BioPatternAlphabet' came up with a help 
page for version 1.4.0, which was probably designed for BioC 1.7/R-2.2.1 
or earlier).

There are four vignettes that come with the package. I am sure that 
reading those should help shed some light on how the package works now.

Best,

Jim


> 
> 
>  
> 
> I am running R 2.4.1, 
> Wimdows XP, Biostrings_2.2.1
> Any help or suggestions that you can
> provide will be greatly appreciated.
> 
> 
>  
> 
> Qing
> 
> 
> 
> 	[[alternative HTML version deleted]]
> 
> 
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623


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