R help - Jan 2007 - reposTools

Dear List,

I tested the example in the reposTools vignette:

library(reposTools);
Loading required package: tools
genRepos("Test 
Repository",
"http://biowww.dfci.harvard.edu/~jgentry/","newRepos");
Error in rep.int(colnames(x), nr) : unimplemented type 'NULL' in
'rep'

Could someone help me out with this one?
I'd appreciate all help....

I am running R 2.4.1 windows XP.

YUE

On 1/28/2007 12:19 AM, qing wrote:
> 
> 
> Dear All?
> 
> 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
> 
> 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.
You should probably ask this on the bioconductor mailing list.  See

http://www.bioconductor.org/docs/mailList.html

for instructions.

Duncan Murdoch

qing wrote:
> 
> 
> Dear All?
> 
> 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

Hi Qing,


"BioPatternAlphabet" was a class defined in Biostrings 1 (Biostrings
version 1.y.z). In Biostrings 2, the class system has changed and you don't
need to create an instance of the DNA alphabet anymore:

  - To create a DNAString object, just do:

      > mydna <- DNAString("AGG-HCNTT")
      > mydna
        9-letter "DNAString" object
      Value: AGG-HCNTT

  - To get the DNA alphabet, call alphabet() on a DNAString object:

      > alphabet(mydna)
       [1] "A" "C" "G" "T" "M"
"R" "S" "V" "W" "Y"
"H" "K" "D" "B" "N"
"-"

    or, if you don't have a DNAString instance yet:

      > DNA_ALPHABET
       [1] "A" "C" "G" "T" "M"
"R" "S" "V" "W" "Y"
"H" "K" "D" "B" "N"
"-"

    Note that the "DNA alphabet" is the "IUPAC Extended Genetic
Alphabet".

  - To get the mapping between the DNA alphabet and the set of ambiguities
    associated to each "extended" letter:

      > IUPAC_CODE_MAP
           A      C      G      T      M      R      W      S      Y      K     
V
         "A"    "C"    "G"    "T"  
"AC"   "AG"   "AT"   "CG"  
"CT"   "GT"  "ACG"
           H      D      B      N
       "ACT"  "AGT"  "CGT" "ACGT"

  - For more details, see:

      > ?DNAString

Cheers,

H.

PS: As Ducan said, the Bioconductor mailing list is a more appropriate place
to ask help about a Bioconductor package.


> 
> 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
> 
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