Re: [R] Paste every two columns together
Hi Kate,
Maybe you want:
seq(2,length(x),by=2)
Jim
On Thu, Jan 29, 2015 at 10:55 AM, Kate Ignatius kate.ignat...@gmail.com wrote:
I have genetic data as follows (simple example, actual data is much larger):
comb =
ID1 A A T G C T G C G T C G T A
ID2 G C T G C C T G C T G T T T
And I wish to get an output like this:
ID1 AA TG CT GC GT CG TA
ID2 GC TG CC TG CT GT TT
That is, paste every two columns together.
I have this code, but I get the error:
Error in seq.default(2, nchar(x), 2) : 'to' must be of length 1
conc - function(x) {
s - seq(2, nchar(x), 2)
paste0(x[s], x[s+1])
}
combn - as.data.frame(lapply(comb, conc), stringsAsFactors=FALSE)
Thanks in advance!
__
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[R] Paste every two columns together
I have genetic data as follows (simple example, actual data is much larger):
comb =
ID1 A A T G C T G C G T C G T A
ID2 G C T G C C T G C T G T T T
And I wish to get an output like this:
ID1 AA TG CT GC GT CG TA
ID2 GC TG CC TG CT GT TT
That is, paste every two columns together.
I have this code, but I get the error:
Error in seq.default(2, nchar(x), 2) : 'to' must be of length 1
conc - function(x) {
s - seq(2, nchar(x), 2)
paste0(x[s], x[s+1])
}
combn - as.data.frame(lapply(comb, conc), stringsAsFactors=FALSE)
Thanks in advance!
__
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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.
Re: [R] Paste every two columns together
eek!
Chel Hee,anything that complicated should engender fear and trembling.
Much simpler and more efficient (if I understand correctly)
i - seq.int(1L,length(ID1),by = 2L)
paste0(ID1[i],ID1[i+1])
That gives a vector of paired letters. If you want a single character
string, just collapse with a (space):
paste0(ID1[i],ID1[i+1],collapse= )
Cheers,
Bert
Bert Gunter
Genentech Nonclinical Biostatistics
(650) 467-7374
Data is not information. Information is not knowledge. And knowledge
is certainly not wisdom.
Clifford Stoll
On Wed, Jan 28, 2015 at 7:41 PM, Chel Hee Lee chl...@mail.usask.ca wrote:
I am using just the first row of your data (i.e. ID1).
ID1 - c(A, A, T, G, C, T, G, C, G, T, C, G, T,
A)
do.call(c,lapply(tapply(ID1, gl(7,2), c), paste, collapse=))
1234567
AA TG CT GC GT CG TA
Is this what you are looking for? I hope this helps.
Chel Hee Lee
On 01/28/2015 05:55 PM, Kate Ignatius wrote:
I have genetic data as follows (simple example, actual data is much
larger):
comb =
ID1 A A T G C T G C G T C G T A
ID2 G C T G C C T G C T G T T T
And I wish to get an output like this:
ID1 AA TG CT GC GT CG TA
ID2 GC TG CC TG CT GT TT
That is, paste every two columns together.
I have this code, but I get the error:
Error in seq.default(2, nchar(x), 2) : 'to' must be of length 1
conc - function(x) {
s - seq(2, nchar(x), 2)
paste0(x[s], x[s+1])
}
combn - as.data.frame(lapply(comb, conc), stringsAsFactors=FALSE)
Thanks in advance!
__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
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.
__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
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.
__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
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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.
Re: [R] Paste every two columns together
Hi Bert! yes, you are VERY correct!!! Why am I making this simple thing
so complicated??? ;) Thank you so much for your nice lesson!
Chel Hee Lee
On 01/28/2015 09:59 PM, Bert Gunter wrote:
eek!
Chel Hee,anything that complicated should engender fear and trembling.
Much simpler and more efficient (if I understand correctly)
i - seq.int(1L,length(ID1),by = 2L)
paste0(ID1[i],ID1[i+1])
That gives a vector of paired letters. If you want a single character
string, just collapse with a (space):
paste0(ID1[i],ID1[i+1],collapse= )
Cheers,
Bert
Bert Gunter
Genentech Nonclinical Biostatistics
(650) 467-7374
Data is not information. Information is not knowledge. And knowledge
is certainly not wisdom.
Clifford Stoll
On Wed, Jan 28, 2015 at 7:41 PM, Chel Hee Lee chl...@mail.usask.ca wrote:
I am using just the first row of your data (i.e. ID1).
ID1 - c(A, A, T, G, C, T, G, C, G, T, C, G, T,
A)
do.call(c,lapply(tapply(ID1, gl(7,2), c), paste, collapse=))
1234567
AA TG CT GC GT CG TA
Is this what you are looking for? I hope this helps.
Chel Hee Lee
On 01/28/2015 05:55 PM, Kate Ignatius wrote:
I have genetic data as follows (simple example, actual data is much
larger):
comb =
ID1 A A T G C T G C G T C G T A
ID2 G C T G C C T G C T G T T T
And I wish to get an output like this:
ID1 AA TG CT GC GT CG TA
ID2 GC TG CC TG CT GT TT
That is, paste every two columns together.
I have this code, but I get the error:
Error in seq.default(2, nchar(x), 2) : 'to' must be of length 1
conc - function(x) {
s - seq(2, nchar(x), 2)
paste0(x[s], x[s+1])
}
combn - as.data.frame(lapply(comb, conc), stringsAsFactors=FALSE)
Thanks in advance!
__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
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.
__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
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.
__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
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.
Re: [R] Paste every two columns together
I am using just the first row of your data (i.e. ID1).
ID1 - c(A, A, T, G, C, T, G, C, G, T, C, G,
T, A)
do.call(c,lapply(tapply(ID1, gl(7,2), c), paste, collapse=))
1234567
AA TG CT GC GT CG TA
Is this what you are looking for? I hope this helps.
Chel Hee Lee
On 01/28/2015 05:55 PM, Kate Ignatius wrote:
I have genetic data as follows (simple example, actual data is much larger):
comb =
ID1 A A T G C T G C G T C G T A
ID2 G C T G C C T G C T G T T T
And I wish to get an output like this:
ID1 AA TG CT GC GT CG TA
ID2 GC TG CC TG CT GT TT
That is, paste every two columns together.
I have this code, but I get the error:
Error in seq.default(2, nchar(x), 2) : 'to' must be of length 1
conc - function(x) {
s - seq(2, nchar(x), 2)
paste0(x[s], x[s+1])
}
combn - as.data.frame(lapply(comb, conc), stringsAsFactors=FALSE)
Thanks in advance!
__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
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.
__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
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.
Re: [R] Paste every two columns together
Kate, here's a solution that uses regular expressions, rather than vector
manipulation:
mystr = ID1 A A T G C T G C G T C G T A
gsub( ([ACGT]) ([ACGT]), \\1\\2, mystr)
[1] ID1 AA TG CT GC GT CG TA
-John
-Original Message-
From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of Chel Hee
Lee
Sent: Wednesday, January 28, 2015 11:07 PM
To: Bert Gunter
Cc: r-help
Subject: Re: [R] Paste every two columns together
Hi Bert! yes, you are VERY correct!!! Why am I making this simple thing so
complicated??? ;) Thank you so much for your nice lesson!
Chel Hee Lee
On 01/28/2015 09:59 PM, Bert Gunter wrote:
eek!
Chel Hee,anything that complicated should engender fear and trembling.
Much simpler and more efficient (if I understand correctly)
i - seq.int(1L,length(ID1),by = 2L)
paste0(ID1[i],ID1[i+1])
That gives a vector of paired letters. If you want a single character
string, just collapse with a (space):
paste0(ID1[i],ID1[i+1],collapse= )
Cheers,
Bert
Bert Gunter
Genentech Nonclinical Biostatistics
(650) 467-7374
Data is not information. Information is not knowledge. And knowledge
is certainly not wisdom.
Clifford Stoll
On Wed, Jan 28, 2015 at 7:41 PM, Chel Hee Lee chl...@mail.usask.ca
wrote:
I am using just the first row of your data (i.e. ID1).
ID1 - c(A, A, T, G, C, T, G, C, G, T, C, G,
T,
A)
do.call(c,lapply(tapply(ID1, gl(7,2), c), paste, collapse=))
1234567
AA TG CT GC GT CG TA
Is this what you are looking for? I hope this helps.
Chel Hee Lee
On 01/28/2015 05:55 PM, Kate Ignatius wrote:
I have genetic data as follows (simple example, actual data is much
larger):
comb =
ID1 A A T G C T G C G T C G T A
ID2 G C T G C C T G C T G T T T
And I wish to get an output like this:
ID1 AA TG CT GC GT CG TA
ID2 GC TG CC TG CT GT TT
That is, paste every two columns together.
I have this code, but I get the error:
Error in seq.default(2, nchar(x), 2) : 'to' must be of length 1
conc - function(x) {
s - seq(2, nchar(x), 2)
paste0(x[s], x[s+1])
}
combn - as.data.frame(lapply(comb, conc), stringsAsFactors=FALSE)
Thanks in advance!
__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
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.
__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
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.
__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
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.
__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
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.
Re: [R] Paste every two columns together
Hi:
Don't know about performance, but this is fairly simple for operating
on atomic vectors:
x - c(A, A, G, T, C, G)
apply(embed(x, 2), 1, paste0, collapse = )
[1] AA GA TG CT GC
Check the help page of embed() for details.
Dennis
On Wed, Jan 28, 2015 at 3:55 PM, Kate Ignatius kate.ignat...@gmail.com wrote:
I have genetic data as follows (simple example, actual data is much larger):
comb =
ID1 A A T G C T G C G T C G T A
ID2 G C T G C C T G C T G T T T
And I wish to get an output like this:
ID1 AA TG CT GC GT CG TA
ID2 GC TG CC TG CT GT TT
That is, paste every two columns together.
I have this code, but I get the error:
Error in seq.default(2, nchar(x), 2) : 'to' must be of length 1
conc - function(x) {
s - seq(2, nchar(x), 2)
paste0(x[s], x[s+1])
}
combn - as.data.frame(lapply(comb, conc), stringsAsFactors=FALSE)
Thanks in advance!
__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
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.
__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
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.
Re: [R] Paste every two columns together
Hi,
Here is my implementation:
combine - function(x){
+ odd - x[1:length(x) %% 2 == 1]
+ even - x[1:length(x) %%2 == 0]
+ paste0(odd,even)}
temp - letters[1:24]
temp
[1] a b c d e f g h i j k l m n o p q r
s t u v w x
combine(temp)
[1] ab cd ef gh ij kl mn op qr st uv wx
--
View this message in context:
http://r.789695.n4.nabble.com/Paste-every-two-columns-together-tp4702429p4702433.html
Sent from the R help mailing list archive at Nabble.com.
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