Hi Nenad, I was using "alphabetFrequency" but your advice to use "alphabetByCycle" was very helpful for my purposes. Thanks Ali
________________________________ From: Nenad Bartonicek <[email protected]> Cc: [email protected] 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: [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
