[Bioc-sig-seq] frequency of A, C, G, T

[Patrick Aboyoun]

Ali,
Biostrings's consensusMatrix method for XStringSet (e.g. DNAStringSet) 
objects performs the same operation as ShortReads's alphabetByCycle, in 
case you were looking for non-ShortRead alternatives.


Patrick



Ali Mohamadian wrote:
> Hi Nenad,
> I was using "alphabetFrequency"  but your advice to use "alphabetByCycle" was very helpful for my purposes.
> Thanks
> Ali
>
>
> ________________________________
> From: Nenad Bartonicek <nenad at ebi.ac.uk>
>
> Cc: bioc-sig-sequencing at r-project.org
> Sent: Thursday, August 27, 2009 11:36:36 AM
> Subject: RE: frequency of A, C, G, T
>
>
> Hi Ali,
>
> There is a function "alphabetFrequency" in the package Biostrings.
> If you were thinking of the total frequency of letters, there is also a function "alphabetByCycle" in the package ShortRead.
>
> Hope it helps,
>
> Nenad
>
> Date: Thu, 27 Aug 2009 01:45:48 -0700 (PDT)
>
>   
>> Subject: [Bioc-sig-seq] frequency of A, C, G, T
>> To: bioc-sig-sequencing at r-project.org
>> Message-ID: <120808.21354.qm at web34203.mail.mud.yahoo.com>
>> Content-Type: text/plain
>>
>> Hi All,
>> I wonder is there any R function to give me the frequency of  A,C,G and T(and  also a,c,g,t) in my reads?
>> Data look like
>> chrY  46418   46469   cgaCGTtcCttcaggcAaagCGCtTGCcCAAatTgCcTTTTtcCCGTCCAC                0 - 46418    46469   0,0,255
>> chrY  119520 119570 AAGGATGGACCATCTTGTgATTGCCATATCCAgggaTCCATCCCATgatca     0 + 119520 119570  255,0,0
>> chrY  119740 119791 aCCCAAGGAGCtAAAGGGATCTGCGaCCCTATAGGTGGAACAACATTATGA 0 - 119740  119791  0,0,255
>> chrY  119740 119791 acccAAGGagctAAAGggatatgcGacccTatAgGtGGAacAacATTatga                   0 - 119740  119791  0,0,255
>> chrY  150045 150096 ttAtTAAGAAAAAttcAGGTAAATGGAGactCGtACAGGACCTTAGAAAAA       0 - 150045  150096   0,0,255
>> chrY  190995 191046 ggatggacacacacacaCacacaCaCACACACACACACACACaCACACgCA              0 - 190995  191046   0,0,255
>> chrY  198579 198629 GTTGCTGGGAtTTGAACTCAGGACCTTTGGAaGAGCAATCGGTGCTCTTaa   0 + 198579 198629   255,0,0
>> chrY  237529 237579 AAACTCAGAAATCTGCCTGCCTCTGCCTCCCAAGTgCTGGGaTTAAAgGcC   0 + 237529 237579   255,0,0
>>  
>> Thanks
>> Ali
>>
>>     
>
>
> Nenad Bartonicek
> PhD student, Enright group
> European Bioinformatics Institute
> Hinxton
> Cambridge
> CB10 1SD
> United Kingdom
> tel: +44-755-435-9057
>
>
>
>       
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