R help - Jul 2008 - counting number of "G" in "TCGGGGGACAATCGGTAACCCGTCT"

Any better solution than this ? 
 
sum(strsplit("TCGGGGGACAATCGGTAACCCGTCT", "")[[1]] ==
"G")
_________________________________________________________________


	[[alternative HTML version deleted]]

Daren Tan <daren76 <at> hotmail.com> writes:
 > Any better solution than this ? 
> sum(strsplit("TCGGGGGACAATCGGTAACCCGTCT", "")[[1]] ==
"G")
Try

table(strsplit("TCGGGGGACAATCGGTAACCCGTCT", ""))

A C G T 
5 7 8 5 
 and get all 4 at once.

HTH

-- 
Ken Knoblauch
Inserm U846
Institut Cellule Souche et Cerveau
D?partement Neurosciences Int?gratives
18 avenue du Doyen L?pine
69500 Bron
France
tel: +33 (0)4 72 91 34 77
fax: +33 (0)4 72 91 34 61
portable: +33 (0)6 84 10 64 10
http://www.sbri.fr

Seems like you can do:

library("matchprobes")   # on Bioconductor
countbases("TCGGGGGACAATCGGTAACCCGTCT")[,"G"]

The catch is that it only counts A, C, G, and T:s and no other symbols.

/Henrik

On Tue, Jul 15, 2008 at 8:27 AM, Daren Tan <daren76 at hotmail.com>
wrote:
>
> Any better solution than this ?
>
> sum(strsplit("TCGGGGGACAATCGGTAACCCGTCT", "")[[1]] ==
"G")
> _________________________________________________________________
>
>
>        [[alternative HTML version deleted]]
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>

Hi,

And the Bioconductor package "Biostrings" is the place to go for any
serious work with sequences.
-- 
Best wishes
 Wolfgang

------------------------------------------------------------------
Wolfgang Huber  EBI/EMBL  Cambridge UK  http://www.ebi.ac.uk/huber


15/07/2008 16:43 Henrik Bengtsson scripsit
> Seems like you can do:
> 
> library("matchprobes")   # on Bioconductor
> countbases("TCGGGGGACAATCGGTAACCCGTCT")[,"G"]
> 
> The catch is that it only counts A, C, G, and T:s and no other symbols.
> 
> /Henrik
> 
> On Tue, Jul 15, 2008 at 8:27 AM, Daren Tan <daren76 a hotmail.com>
wrote:
>> Any better solution than this ?
>>
>> sum(strsplit("TCGGGGGACAATCGGTAACCCGTCT", "")[[1]]
== "G")
>> _________________________________________________________________

Henrik,
As Wolfgang mentioned, the Biostrings package in Bioconductor has a 
number of sequence manipulation functions. The alphabetFrequency 
function would get you what you need.

 > library(Biostrings)
 > alphabetFrequency(DNAString("TCGGGGGACAATCGGTAACCCGTCT"))
A C G T M R W S Y K V H D B N - +
5 7 8 5 0 0 0 0 0 0 0 0 0 0 0 0 0
 > alphabetFrequency(DNAString("TCGGGGGACAATCGGTAACCCGTCT"),
baseOnly =
TRUE)
    A     C     G     T other
    5     7     8     5     0


Patrick


Wolfgang Huber wrote:
> Hi,
>
> And the Bioconductor package "Biostrings" is the place to go for
any
> serious work with sequences.
>

Daren,

Not sure if it is any easier, but another solution is:


code <- unlist(strsplit("TCGGGGGACAATCGGTAACCCGTCT",""))

length(grep("[G]",code)) 


Steve 


-----Original Message-----
From: r-help-bounces at r-project.org [mailto:r-help-bounces at r-project.org]
On Behalf Of Daren Tan
Sent: Tuesday, July 15, 2008 11:28 AM
To: r-help at stat.math.ethz.ch
Subject: [R] counting number of "G" in
"TCGGGGGACAATCGGTAACCCGTCT"


Any better solution than this ? 
 
sum(strsplit("TCGGGGGACAATCGGTAACCCGTCT", "")[[1]] ==
"G")
_________________________________________________________________


	[[alternative HTML version deleted]]

______________________________________________
R-help at r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.