[BioC] Question about Rle

[Valerie Obenchain]

On 07/31/2014 11:41 AM, Valerie Obenchain wrote:
> Hi,
>
> The standard Bioconductor container for sequences are the XString


Sorry, the 'BA' below is a typo and should be 'BS'. The BS class is for 
any long sequence of characters vs the more biologically oriented DNA, 
RNA and AA types.

Valerie

> family. BA, DNA, RNA and AA types are supported. See the man page for
> details on subsetting and manipulation.


>
> library(Biostrings)
> ?XString
> ?DNAString
>
> You can represent a single sequence
> dna <- DNAString("ATGTATCC")
>>> dna
>>   8-letter "DNAString" instance
>> seq: ATGTATCC
>>> dna[3]
>>   1-letter "DNAString" instance
>> seq: G
>
> or a set of sequences.
> dnast <- DNAStringSet(c("AT", "G", "ATC", "C"))
>>> dnast
>>   A DNAStringSet instance of length 4
>>     width seq
>> [1]     2 AT
>> [2]     1 G
>> [3]     3 ATC
>> [4]     1 C
>
> Methods for operating on sequences are built on the XString framework,
> not Rles. If you really wanted to represent a sequence as an Rle it
> would be a character Rle and constructed in the same way the other
> atomic types are. See ?Rle.
>
> rle <- Rle(c("A", "T", "G", "T", "A", "T", "C"), c(rep(1, 6), 2))
>>> rle
>> character-Rle of length 8 with 7 runs
>>   Lengths:   1   1   1   1   1   1   2
>>   Values : "A" "T" "G" "T" "A" "T" "C"
>>> rle[3]
>> character-Rle of length 1 with 1 run
>>   Lengths:   1
>>   Values : "G"
>
>
> Valerie
>
>
> On 07/29/2014 04:04 AM, Asma rabe wrote:
>> Hi All,
>>
>>
>> I have a question DNA sequence encoding in Rle objects
>>
>>
>> #-------------------------
>>
>>> From IRanges vignette
>>
>>
>>   the sequence *{*1, 1, 1, 2, 3, 3*} * can be represented as values
>>
>> = *{*1, 2, 3*}* , run lengths = {3, 1, 2*}* .
>>
>>
>> #---------------------------
>>
>> suppose we have a sequence of chr1 from pos 1-8     ATGTATCC. How it
>> can be
>> as Rle object Rle the so that it is recognized at pos 3 for instance the
>> nuceoyide is G for comparison with reference genome?
>>
>>
>> Thank you very much in advance.
>>
>>     [[alternative HTML version deleted]]
>>
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>
>