Hi Herve,

Thanks so much for your time and advices. Best,

Steve

2011/1/28 Hervé Pagès <hpages@fhcrc.org>

> Hi Steve,
>
>
> On 01/27/2011 10:37 PM, Steve Shen wrote:
>
>> Hi Herve,
>>
>> Sorry for bothering you again. With you help, I was able to build this
>> BSgenome data package. Now it brings me another level of problem. How do
>> I manipulate the sequences since it is quite different from the examples
>> in your documentation? For example, how can I find the sequences that
>> length is 1000bp or less? I have issued couple of commands and list the
>> output below. Thanks so much for your help. By the way, do you guys
>> offer a training class in a near future?
>>
>> Steve
>>
>>  > seq <- CFlo$cflo_v3.3.fold
>>  > str(seq)
>> Formal class 'DNAStringSet' [package "Biostrings"] with 5 slots
>>   ..@ pool           :Formal class 'SharedRaw_Pool' [package "IRanges"]
>> with 2 slots
>>   .. .. ..@ xp_list                    :List of 1
>>   .. .. .. ..$ :<externalptr>
>>   .. .. ..@ .link_to_cached_object_list:List of 1
>>   .. .. .. ..$ :<environment: 0x7a68ec0>
>>   ..@ ranges         :Formal class 'GroupedIRanges' [package "IRanges"]
>> with 7 slots
>>   .. .. ..@ group          : int [1:24026] 1 1 1 1 1 1 1 1 1 1 ...
>>   .. .. ..@ start          : int [1:24026] 1 372 921 1459 2139 3015
>> 17388 34650 67069 78840 ...
>>   .. .. ..@ width          : int [1:24026] 371 549 538 680 876 14373
>> 17262 32419 11771 16416 ...
>>   .. .. ..@ NAMES          : chr [1:24026] "scaffold9" "scaffold12"
>> "scaffold16" "scaffold2" ...
>>   .. .. ..@ elementMetadata: NULL
>>   .. .. ..@ elementType    : chr "integer"
>>   .. .. ..@ metadata       : list()
>>   ..@ elementMetadata: NULL
>>   ..@ elementType    : chr "DNAString"
>>   ..@ metadata       : list()
>>
>>  > seq
>>   A DNAStringSet instance of length 24026
>>           width seq                                         names
>>     [1]     371 GTATATAAATAAAAATCTTA...AAACTGTCATACAAACAGTT scaffold9
>>     [2]     549 TATCTATATTTTATAAATTA...GAAATTTTTATAAGCTTATT scaffold12
>>     [3]     538 ATAATGAGCAAGAATAAATT...TACATATTAGTTGGTTCTCT scaffold16
>>     [4]     680 CGCCAATCTATGAAGACGAA...GATCATGAATTCAAATGGGA scaffold2
>>     [5]     876 CACATGATTTATTTGCAGAA...CGCCGATTGTACATGTGATA scaffold4
>>     [6]   14373 CGTTCGGTCTGCTCAATGTT...ACTGCCGCATGTTTAGCATT scaffold20
>>     [7]   17262 ATTATCTACAAGCTTGGTAA...TAGGAGCCGCCCGACCGCTC scaffold10
>>     [8]   32419 AGAGAAGGAACAGAGAAGAA...TACTTTTGTTATTTTAGAAG scaffold11
>>     [9]   11771 CAATGTCAAACTGATAACAT...GTCTGATTAGGATTCATCGC scaffold24
>>     ...     ... ...
>> [24018]    5878 TTTTTTTTTTTTTCGAAAAT...ATAGTTATTTTACATATTAG C4054188
>> [24019]    5945 TTATATTAGATTCTTAAAGT...AAATAATAAATAATAAATAA C4054414
>> [24020]    5777 ATAATAATACCGTTCACAAG...CGATGCGTCCTTTTCTTTTT C4053796
>> [24021]    6301 TTTATTATTTATTAAGCTTT...TATTTTACGTAGCGAAAAAA C4055556
>> [24022]    6987 TAAAAAAAATAGTTATATTT...AGAAATTTATTATTATTATT C4057106
>> [24023]    7532 TCTCAGGGGCTGGTCTGCCT...CGGACGCGTGGAGAGAGTCA C4058062
>> [24024]    9748 TCCTCGCGCTTACCGTTTGA...AAAAATTTGGTTGCGTTAAT C4059958
>> [24025]   32760 GCTTCCGAGGTCGGGGACGC...AACGACGGTTCGCCTGCTAT scaffold5109
>> [24026]   18211 TTATTTATTAAAATAAATAA...AGCGAGGGTGCGGCCCCGGC scaffold4322
>>
>>
> 'seq' is a DNAStringSet object so you could start by looking at the
> man page for those objects (?DNAStringSet) for the basics of how to
> manipulate yours. This is a good starting point. From there you
> will eventually end up visiting other man pages in the Biostrings
> package by following the suggestions given in the "See also" section.
> Biostrings has a lot of man pages! Most man pages provide a lot of
> examples that you will definitely want to look at.
>
> For your particular problem of selecting the elements that are
> <= 1000bp, just do 'seq[width(seq) <= 1000]'.
>
> Please see our website for course announcements:
>
>  http://bioconductor.org/
>
> Cheers,
> H.
>
>
>
> --
> Hervé Pagès
>
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M2-B876
> P.O. Box 19024
> Seattle, WA 98109-1024
>
> E-mail: hpages@fhcrc.org
> Phone:  (206) 667-5791
> Fax:    (206) 667-1319
>

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