Hi Herve,
Thanks for your response. System is considering as characters in the
dataframe.So I was thinking of using them as vectors.But if I scan as
seperate elements and convert them to numeric using lapply.It becomes atomic
numeric.How do I make them as vectors without using combining fuction as
c(1,2,3)?I am basically new to sequences using R.So will read
write.XStringSet().
Thanks,
Viritha
2011/8/16 Hervé Pagès <hpages@fhcrc.org>

> Hi Viritha,
>
>
> On 11-08-16 08:01 AM, viritha kaza wrote:
>
>> Hi group,
>> I am interested in retrieving about 2000 sequences with the specific
>> chromosome number,start and end site.
>> I was thinking of using BSgenome package for this.
>>
>>
>> source("http://bioconductor.**org/biocLite.R<http://bioconductor.org/biocLite.R>
>>> ")
>>>
>>
>> biocLite("BSgenome","BSgenome.**Hsapiens.UCSC.hg19")
>>>
>>
>> library(BSgenome)
>>>
>>
>> library("BSgenome.Hsapiens.**UCSC.hg19")
>>>
>>
>> myseq<- getSeq(Hsapiens,"chr2",start=**10000,end=10020)
>>>
>>
>> # this would work for specific values.
>>
>> #So I tried to use a dataframe where it would retrieve chromosome number
>> from by using
>>
>> full<-as.matrix(read.table(“**test_seq.txt”,sep=’\t’,quote=”**
>>> ”,header=True,
>>>
>> as.is=TRUE))
>>
>
> Why are you doing as.matrix here? Do you *really* want all the columns
> to be coerced to the same type? (which in your case is probably
> character because you have already one column of that type).
>
>
>
>> full.df<-data.frame(full)
>>>
>>
> So you're back to a data.frame, except that now all the columns are
> character vectors :-/
>
>
>
>> # test_seq contains this information
>>
>> #chromosome Start End
>> #chr2 10000 10020
>> #chr3 10000 10020
>>
>
> Why not copy and paste what you get when you just type full.df? That
> way would know exactly what you ended up with (if full.df is too big,
> just show us the output of head(full.df)).
> Anyway, it looks like you'll have to get rid of those #. Otherwise
> passing Hsapiens,full.df$chromosome to getSeq() with those # in it
> will surely cause problems.
>
>
>
>> myseq<- getSeq(Hsapiens,full.df$**chromosome,start=10000,end=**10020)
>>>
>>
>> #but then when I use start=full.df$Start. It naturally throws an error
>> saying 'start' must be a vector of integers
>>
>> Questions:
>>
>> How Do I handle this?
>>
>
> By having full.df$Start be a vector of integers and also by reading
> the man page for getSeq().
>
>
>
>> Does start here mean that each chromosome numbering starts from 1?
>>
>
> Yes, the first base at the 5' end of the + strand (or 3' end of the -
> strand) is considered to be position 1.
>
>
>
>> How do I split each sequence retrieved and create as fasta format (>)with
>> sequence name attached to them retrieved from my input file?
>>
>
> How do you want to "split" each sequence retrieved? As a good starting
> point you could have a look at write.XStringSet(). Note that
> the names you put on your DNAStringSet object will be used as the
> record description lines in the resulting FASTA file.
>
> Cheers,
> H.
>
>
>>
>>
>> sessionInfo()
>>>
>>
>> R version 2.13.0 (2011-04-13)
>> Platform: i386-pc-mingw32/i386 (32-bit)
>>
>> locale:
>> [1] LC_COLLATE=English_United States.1252
>> [2] LC_CTYPE=English_United States.1252
>> [3] LC_MONETARY=English_United States.1252
>> [4] LC_NUMERIC=C
>> [5] LC_TIME=English_United States.1252
>>
>> attached base packages:
>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>
>> other attached packages:
>> [1] BSgenome.Hsapiens.UCSC.hg19_1.**3.17 BSgenome_1.20.0
>> [3] Biostrings_2.20.1                  GenomicRanges_1.4.6
>> [5] IRanges_1.10.4
>>
>> loaded via a namespace (and not attached):
>> [1] tools_2.13.0
>>
>>
>>
>> Waiting for your suggestions,
>>
>> Thank you,
>>
>> Viritha
>>
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>>
>>
>>
>>
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>>
>
>
> --
> Hervé Pagès
>
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M1-B514
> P.O. Box 19024
> Seattle, WA 98109-1024
>
> E-mail: hpages@fhcrc.org
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>

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