BSgenome data loading problem for applying in biostrings package function
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21-01-2021 - |
Pregunta
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$chr3R
Error: object 'Dmelanogaster' not found
> Lpattern <- "AGCTCCGAG"
> Rpattern <- "TTGTTCACA"
> matchLRPatterns(Lpattern, Rpattern, 500, subject) # 1 match
Error in function (classes, fdef, mtable) :
unable to find an inherited method for function "matchLRPatterns", for signature "standardGeneric"
I will appreciate your help. Can you try in your computer to see if this works for your? what could be potential problem.
Solución
Thanks to Roman Lustrik the following codes works:
source("bioconductor.org/biocLite.R";)
biocLite("BSgenome.Dmelanogaster.UCSC.dm3")
library(BSgenome.Dmelanogaster.UCSC.dm3)
subject <- Dmelanogaster$chr3R
Lpattern <- "AGCTCCGAG"
Rpattern <- "TTGTTCACA"
matchLRPatterns(Lpattern,
Rpattern, 500, subject) # 1 match
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