it is pretty enough for me.  Thanks

----- Original Message ----
From: Martin Morgan <mtmorgan@fhcrc.org>
To: joseph <jdsandjd@yahoo.com>
Cc: r-help@r-project.org
Sent: Friday, February 22, 2008 6:41:41 PM
Subject: Re: [R] counting sequence mismatches


One 
kind 
of 
ugly 
solution

 
> 
d.f=data.frame(seq1, 
seq2, 
stringsAsFactors=FALSE)
 
> 
d.f[["nMismatch"]] 
<- 
with(d.f, 
{
+  
 
m 
<- 
mapply("!=", 
strsplit(seq1, 
""), 
strsplit(seq2, 
""))
+  
 
colSums(m)
+ 
})

Check 
out 
the 
Bioconductor 
Biostrings 
package, 
especially 
the 
version 
available 
with 
the 
development 
version 
of 
R, 
for 
DNA 
string 
algorithms.

Martin

joseph 
wrote:
> 
Hello
> 
I 
have 
2 
columns 
of 
short 
sequences 
that 
I 
would 
like 
to 
compare 
and 
count 
the 
number 
of 
mismatches 
and  
record 
the  
number 
of 
mismatches 
in 
a 
new 
column. 
The 
sequences 
are 
part 
of 
a 
data 
frame 
that 
looks 
like 
this:
> 
seq1=c("CGGTGTAGAGGAAAAAAAGGAAACAGGAGTTC","CGGTGGTCAGTCTGGGACCTGGGCAGCAGGCT", 
"CGGGCCTCTCGGCCTGCAGCCCCCAACAGCCA")
> 
seq2=c("AGGTGTAGAGGAAAAAAAGGAAACAGGAGTTC","CAGTGGTCAGTCTGGGACCTGGGCATCAGGCT", 
"CGGGCCTCTCGGCCTGCAGCCCCCAACAGCCA")
> 
d.f=data.frame(seq1, 
seq2)
> 
thank 
you 
for 
your 
help
> 
Joseph
> 
> 
> 
> 
> 
> 
>  
  
  
 
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> 
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> 
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> 
PLEASE 
do 
read 
the 
posting 
guide 
http://www.R-project.org/posting-guide.html
> 
and 
provide 
commented, 
minimal, 
self-contained, 
reproducible 
code.







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