reading fasta file into R
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Guest User ★ 12k
@guest-user-4897
Last seen 6.6 years ago
Hi, i am a learner of R and bioconductir, biostrings etc. i want to read a fasta file in R, the file is saved on my desktop. please guide me how can i do that,i have seen few manuals but still its confusing for me. -- output of sessionInfo(): fdf -- Sent via the guest posting facility at bioconductor.org.
Biostrings Biostrings • 17k views
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@vincent-j-carey-jr-4
Last seen 7 days ago
United States
install Biostrings package; study the Installation node of bioconductor.orgif this has not occurred issue the commands library(Biostrings) ?read.DNAStringSet look at the example towards the end of the help page do read and abide by the posting guide at bioconductor.org if you have further questions On Tue, Jul 24, 2012 at 5:25 AM, Tahir Mujtaba [guest] < guest@bioconductor.org> wrote: > > Hi, > > i am a learner of R and bioconductir, biostrings etc. > i want to read a fasta file in R, the file is saved on my desktop. > please guide me how can i do that,i have seen few manuals but still its > confusing for me. > > -- output of sessionInfo(): > > fdf > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
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You can also directly run some examples from those help pages; library(ShortRead) example(readFasta) example(read.DNAStringSet) Note, example(read.DNAStringSet) depends on the package 'BSgenome.Celegans.UCSC.ce2' , which is only a suggested package. Marcus On Wed, Jul 25, 2012 at 12:51 AM, Vincent Carey <stvjc@channing.harvard.edu>wrote: > install Biostrings package; study the Installation node of > bioconductor.orgif this has not occurred > > issue the commands > > library(Biostrings) > ?read.DNAStringSet > > look at the example towards the end of the help page > > do read and abide by the posting guide at bioconductor.org if you have > further questions > > On Tue, Jul 24, 2012 at 5:25 AM, Tahir Mujtaba [guest] < > guest@bioconductor.org> wrote: > > > > > Hi, > > > > i am a learner of R and bioconductir, biostrings etc. > > i want to read a fasta file in R, the file is saved on my desktop. > > please guide me how can i do that,i have seen few manuals but still its > > confusing for me. > > > > -- output of sessionInfo(): > > > > fdf > > > > -- > > Sent via the guest posting facility at bioconductor.org. > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@r-project.org > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
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