应用于biostrings包函数的BSgenome数据加载问题

发布于 2024-12-05 01:26:55 字数 767 浏览 2 评论 0原文

我安装了 BSgenome 似乎可以工作，但无法加载库。以下代码来自 Biostrings 包，

     > require(BSgenome) 
     > require(Biostrings)      
    >    library(BSgenome.Dmelanogaster.UCSC.dm3)
    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"

我将感谢您的帮助。您可以在您的计算机上尝试一下，看看这是否适合您？可能存在什么潜在问题。

原文

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)
    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.

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魔法少女 2024-12-12 01:26:55

感谢 Roman Lustrik，以下代码可以运行：

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

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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