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 <[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
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