R help - Feb 2009 - Filtering a dataset's columns by another dataset's column names

Hello all,

I hope some of you can come to my rescue, yet again.

I have two genetic datasets, and I want one of the datasets to have only the
columns that are in common with the other dataset.
Here is a toy example (my real datasets have hundreds of columns):

Dataset 1:

Individual    SNP1    SNP2    SNP3    SNP4    SNP5
1    A    G    T    C    A
2    T    C    A    G    T
3    A    C    T    C    A

Dataset 2:

Individual    SNP1    SNP3    SNP5    SNP6    SNP7
4    A    T    T    G    C
5    T    A    A    G    G
6    A    A    T    C    G

I want Dataset1 to have only columns that are also represented in Dataset 2,
i.e., I want to generate a new Dataset 3 that looks like this:

Individual    SNP1    SNP3    SNP5
1    A    T    A
2    T    A    T
3    A    T    A

Does anyone know how I could do this? Keep in mind that this is not a simple
merge, as in the "merge" function.

Thanks very much for your help everyone.
Josh B.



      
	[[alternative HTML version deleted]]

Try this:

d1[,intersect(names(d1),names(d2))]

HTH, Brian

-----Original Message-----
From: r-help-bounces at r-project.org [mailto:r-help-bounces at r-project.org]
On Behalf Of Josh B
Sent: Friday, February 27, 2009 12:28 PM
To: R Help
Subject: [R] Filtering a dataset's columns by another dataset's column
names


Hello all,

I hope some of you can come to my rescue, yet again.

I have two genetic datasets, and I want one of the datasets to have only
the columns that are in common with the other dataset. 
Here is a toy example (my real datasets have hundreds of columns):

Dataset 1:

Individual    SNP1    SNP2    SNP3    SNP4    SNP5
1    A    G    T    C    A
2    T    C    A    G    T
3    A    C    T    C    A

Dataset 2:

Individual    SNP1    SNP3    SNP5    SNP6    SNP7
4    A    T    T    G    C
5    T    A    A    G    G
6    A    A    T    C    G

I want Dataset1 to have only columns that are also represented in
Dataset 2, i.e., I want to generate a new Dataset 3 that looks like
this:

Individual    SNP1    SNP3    SNP5
1    A    T    A
2    T    A    T
3    A    T    A

Does anyone know how I could do this? Keep in mind that this is not a
simple merge, as in the "merge" function.

Thanks very much for your help everyone.
Josh B.



      
	[[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.

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on 02/27/2009 11:27 AM Josh B wrote:
> Hello all,
> 
> I hope some of you can come to my rescue, yet again.
> 
> I have two genetic datasets, and I want one of the datasets to have only
the columns that are in common with the other dataset.
> Here is a toy example (my real datasets have hundreds of columns):
> 
> Dataset 1:
> 
> Individual    SNP1    SNP2    SNP3    SNP4    SNP5
> 1    A    G    T    C    A
> 2    T    C    A    G    T
> 3    A    C    T    C    A
> 
> Dataset 2:
> 
> Individual    SNP1    SNP3    SNP5    SNP6    SNP7
> 4    A    T    T    G    C
> 5    T    A    A    G    G
> 6    A    A    T    C    G
> 
> I want Dataset1 to have only columns that are also represented in Dataset
2, i.e., I want to generate a new Dataset 3 that looks like this:
> 
> Individual    SNP1    SNP3    SNP5
> 1    A    T    A
> 2    T    A    T
> 3    A    T    A
> 
> Does anyone know how I could do this? Keep in mind that this is not a
simple merge, as in the "merge" function.
> 
> Thanks very much for your help everyone.
> Josh B.
Same.Cols <- intersect(names(DF1), names(DF2))
> Same.Cols
[1] "Individual" "SNP1"       "SNP3"      
"SNP5"
> rbind(DF1[, Same.Cols], DF2[, Same.Cols])
  Individual SNP1 SNP3 SNP5
1          1    A    T    A
2          2    T    A    T
3          3    A    T    A
4          4    A    T    T
5          5    T    A    A
6          6    A    A    T


See ?intersect, which gives you the common column names, which you can
then use in rbind().

HTH,

Marc Schwartz

Dear Josh,
Try this:

dataset1[,colnames(dataset1) %in% colnames(dataset2)]

Take a look at ?colnames and ?"%in%" for more information.

HTH,

Jorge


On Fri, Feb 27, 2009 at 12:27 PM, Josh B <joshb41@yahoo.com> wrote:
> Hello all,
>
> I hope some of you can come to my rescue, yet again.
>
> I have two genetic datasets, and I want one of the datasets to have only
> the columns that are in common with the other dataset.
> Here is a toy example (my real datasets have hundreds of columns):
>
> Dataset 1:
>
> Individual    SNP1    SNP2    SNP3    SNP4    SNP5
> 1    A    G    T    C    A
> 2    T    C    A    G    T
> 3    A    C    T    C    A
>
> Dataset 2:
>
> Individual    SNP1    SNP3    SNP5    SNP6    SNP7
> 4    A    T    T    G    C
> 5    T    A    A    G    G
> 6    A    A    T    C    G
>
> I want Dataset1 to have only columns that are also represented in Dataset
> 2, i.e., I want to generate a new Dataset 3 that looks like this:
>
> Individual    SNP1    SNP3    SNP5
> 1    A    T    A
> 2    T    A    T
> 3    A    T    A
>
> Does anyone know how I could do this? Keep in mind that this is not a
> simple merge, as in the "merge" function.
>
> Thanks very much for your help everyone.
> Josh B.
>
>
>
>
>        [[alternative HTML version deleted]]
>
> ______________________________________________
> R-help@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.
>
	[[alternative HTML version deleted]]

So you want the data that is in Dataset 1 but only the column names  
that are also in Dataset 2:

How about:

  subset(DS1, select = names(DS1) %in% names(DS2) )

 > DS1 <-read.table(textConnection("Individual    SNP1    SNP2     
SNP3    SNP4    SNP5
+ 1    A    G    T    C    A
+ 2    T    C    A    G    T
+ 3    A    C    T    C    A"),header=TRUE)
 > DS2 <-read.table(textConnection("Individual    SNP1    SNP3     
SNP5    SNP6    SNP7
+ 4    A    T    T    G    C
+ 5    T    A    A    G    G
+ 6    A    A    T    C    G"),header=TRUE)

 > subset(DS1, select= names(DS1) %in% names(DS2) )
   Individual SNP1 SNP3 SNP5
1          1    A    T    A
2          2    T    A    T
3          3    A    T    A

Tested!
-- 
David Winsemius
Heritage Labs

On Feb 27, 2009, at 12:27 PM, Josh B wrote:
> Hello all,
>
> I hope some of you can come to my rescue, yet again.
>
> I have two genetic datasets, and I want one of the datasets to have  
> only the columns that are in common with the other dataset.
> Here is a toy example (my real datasets have hundreds of columns):
>
> Dataset 1:
>
> Individual    SNP1    SNP2    SNP3    SNP4    SNP5
> 1    A    G    T    C    A
> 2    T    C    A    G    T
> 3    A    C    T    C    A
>
> Dataset 2:
>
> Individual    SNP1    SNP3    SNP5    SNP6    SNP7
> 4    A    T    T    G    C
> 5    T    A    A    G    G
> 6    A    A    T    C    G
>
> I want Dataset1 to have only columns that are also represented in  
> Dataset 2, i.e., I want to generate a new Dataset 3 that looks like  
> this:
>
> Individual    SNP1    SNP3    SNP5
> 1    A    T    A
> 2    T    A    T
> 3    A    T    A
>
> Does anyone know how I could do this? Keep in mind that this is not  
> a simple merge, as in the "merge" function.
>
> Thanks very much for your help everyone.
> Josh B.
>
>
>
>
> 	[[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 Josh B,

this looks like homework to me. Please obey the posting rules. I.e., provide
self-contained code/examples and show what the point is at which you are
stuck. 

To solve your problem, you need the "which" and the "names"
function as well
as the %in%  operator. It is then easy to rbind the two datasets once you
have figured out what the common column names are. Please try on your own
first and report back if and where you are stuck along with the
self-contained code. If this is indeed homework, please ask your professor
or teacher.

Example for two simulated datasets:

x=rnorm(30)
dim(x)=c(5,6)
x=data.frame(x)
names(x)=c("a","b","c","x","y","z")

y=rnorm(30)
dim(y)=c(5,6)
y=data.frame(y)
names(y)=c("a","b","d","v","w","x")

Daniel


-------------------------
cuncta stricte discussurus
-------------------------

-----Urspr?ngliche Nachricht-----
Von: r-help-bounces at r-project.org [mailto:r-help-bounces at r-project.org] Im
Auftrag von Josh B
Gesendet: Friday, February 27, 2009 12:28 PM
An: R Help
Betreff: [R] Filtering a dataset's columns by another dataset's column
names

Hello all,

I hope some of you can come to my rescue, yet again.

I have two genetic datasets, and I want one of the datasets to have only the
columns that are in common with the other dataset. 
Here is a toy example (my real datasets have hundreds of columns):

Dataset 1:

Individual    SNP1    SNP2    SNP3    SNP4    SNP5
1    A    G    T    C    A
2    T    C    A    G    T
3    A    C    T    C    A

Dataset 2:

Individual    SNP1    SNP3    SNP5    SNP6    SNP7
4    A    T    T    G    C
5    T    A    A    G    G
6    A    A    T    C    G

I want Dataset1 to have only columns that are also represented in Dataset 2,
i.e., I want to generate a new Dataset 3 that looks like this:

Individual    SNP1    SNP3    SNP5
1    A    T    A
2    T    A    T
3    A    T    A

Does anyone know how I could do this? Keep in mind that this is not a simple
merge, as in the "merge" function.

Thanks very much for your help everyone.
Josh B.



      
	[[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.