it is pretty enough for me. Thanks
----- Original Message ----
From: Martin Morgan <[EMAIL PROTECTED]>
To: joseph <[EMAIL PROTECTED]>
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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