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)
> From: Ali Mohamadian <moham_am@yahoo.com>
> Subject: [Bioc-sig-seq] frequency of A, C, G, T
> To: bioc-sig-sequencing@r-project.org
> Message-ID: <120808.21354.qm@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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