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 <[email protected]> > Subject: [Bioc-sig-seq] frequency of A, C, G, T > To: [email protected] > Message-ID: <[email protected]> > 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 [[alternative HTML version deleted]] _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
