R help - Mar 2010 - tapply syntax

Dear R-help members,

Apologies for the trouble.

I have a question :

Essentially, I have a dataset which stores genetic variations for individual
patients. Each individual patient can have more than one variation, and each
new record corresponds to a new variation (thus, both individual patients
and variations are non-unique).

So the dataset looks something like this ((letters = patients, numbers variation
type).
Patient, Variation Type
A, 1
A, 2
A, 3
B, 1
C, 2
D, 2
D, 3
E, 2
E, 4
F, 4

My final desired output is a data.frame or a vector containing patients,
each corresponding to a desired subset of variations. For e.g., if I only
was interested in variation type 2,3, my output would look like this.

A, 2
B, 0
C, 1
D, 2
E, 1
F, 0.

I am trying to figure out how to use tapply to do this.

It would be something like tapply (Variation Type, Patient, ??? )

I am not sure about the function syntax of ??? to subselect only 2,3, and
have been looking at the r-help.

Sorry! Essentially, I am trying to avoid awkward loops in this whole
process.

Thanks very much for your advice!

Min-Han

	[[alternative HTML version deleted]]

Hi,

I figured a workaround to my problem, but if anyone has any advice on how to
express a function in tapply to achieve the same outcome, that would be
awesome and I'd learn something about functions!

The workaround was
tapply ((data$Variation.Type %in% c(2,3)), data$Patient, sum)

Thanks.

Min-Han

On Fri, Mar 26, 2010 at 12:40 PM, Min-Han Tan
<minhan.science@gmail.com>wrote:
> Dear R-help members,
>
> Apologies for the trouble.
>
> I have a question :
>
> Essentially, I have a dataset which stores genetic variations for
> individual patients. Each individual patient can have more than one
> variation, and each new record corresponds to a new variation (thus, both
> individual patients and variations are non-unique).
>
> So the dataset looks something like this ((letters = patients, numbers >
variation type).
> Patient, Variation Type
> A, 1
> A, 2
> A, 3
> B, 1
> C, 2
> D, 2
> D, 3
> E, 2
> E, 4
> F, 4
>
> My final desired output is a data.frame or a vector containing patients,
> each corresponding to a desired subset of variations. For e.g., if I only
> was interested in variation type 2,3, my output would look like this.
>
> A, 2
> B, 0
> C, 1
> D, 2
> E, 1
> F, 0.
>
> I am trying to figure out how to use tapply to do this.
>
> It would be something like tapply (Variation Type, Patient, ??? )
>
> I am not sure about the function syntax of ??? to subselect only 2,3, and
> have been looking at the r-help.
>
> Sorry! Essentially, I am trying to avoid awkward loops in this whole
> process.
>
> Thanks very much for your advice!
>
> Min-Han
>
	[[alternative HTML version deleted]]

how about:

d1=data.frame(pat=c(rep('a',3),'b','c',rep('d',2),rep('e',2),'f'),var=c(1,2,3,1,2,2,3,2,4,4))
ds=set(d1,var %in% c(2,3))
with(ds,tapply(var,pat,FUN=length))

hth,
David Freedman, CDC, Atlanta
-- 
View this message in context:
http://n4.nabble.com/tapply-syntax-tp1692503p1692553.html
Sent from the R help mailing list archive at Nabble.com.