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BSgenome data loading problem for applying in biostrings package function

开发者 https://www.devze.com 2023-04-05 09:34 出处:网络
I installed BSgenome seems working but I am not able to load library. The following code are fromBiostrings package

I installed BSgenome seems working but I am not able to load library. The following code are from Biostrings package

     > require(BSgenome) 
     > require(Biostrings)      
    >    library(BSgenome.Dmelanogaster.UCSC.dm3)
 开发者_StackOverflow   Error in library(BSgenome.Dmelanogaster.UCSC.dm3) : 
      there is no package called 'BSgenome.Dmelanogaster.UCSC.dm3'
    >   subject <- Dmelanogaster$chr3R
    Error: object 'Dmelanogaster' not found
    >   Lpattern <- "AGCTCCGAG"
    >   Rpattern <- "TTGTTCACA"
    >   matchLRPatterns(Lpattern, Rpattern, 500, subject) # 1 match
    Error in function (classes, fdef, mtable)  : 
      unable to find an inherited method for function "matchLRPatterns", for signature "standardGeneric"

I will appreciate your help. Can you try in your computer to see if this works for your? what could be potential problem.


Thanks to Roman Lustrik the following codes works:

source("bioconductor.org/biocLite.R";) 
biocLite("BSgenome.Dmelanogaster.UCSC.dm3") 
library(BSgenome.Dmelanogaster.UCSC.dm3) 
subject <- Dmelanogaster$chr3R 
Lpattern <- "AGCTCCGAG" 
Rpattern <- "TTGTTCACA" 
matchLRPatterns(Lpattern, 
Rpattern, 500, subject) # 1 match 
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