[R] Mean of matched data

[Peter Ehlers]

On 2012-07-18 04:27, Rui Barradas wrote:
> Helo,
>
> All problems should be easy.
>
>
> d <- read.table(text="
> gene variable value gender line rep
> 1 CG10000 X208.F1.30456 4.758010 Female 208 1
> 2 CG10000 X365.F2.30478 4.915395 Female 365 2
> 3 CG10000 X799.F2.30509 4.641636 Female 799 2
> 4 CG10000 X306.M2.32650 4.550676 Male 306 2
> 5 CG10000 X712.M2.30830 4.633811 Male 712 2
> 6 CG10000 X732.M2.30504 4.857564 Male 732 2
> 7 CG10000 X707.F1.31120 5.104165 Female 707 1
> 8 CG10000 X514.F2.30493 4.730814 Female 514 2
> ", header=TRUE)
>
> # See what we have
> str(d)
>
> # or put function(x) ...etc... in the aggregate
> f <- function(x) c(mean=mean(x), sd=sd(x))
> aggregate(value ~ gene + gender, data = d, f)
>
>
> Hope this helps,
>
> Rui Barradas

I read the request a bit differently; we can use ave()
to generate the requested new variables:

d1 <- transform(d,
            MN = ave(value, gene, gender),
            SD = ave(value, gene, gender, FUN = sd))

Or use within() instead of transform().

Peter Ehlers

> Em 18-07-2012 10:54, robgriffin247 escreveu:
>> Hi
>> I think/hope there will be a simple solution to this but google-ing has
>> provided no answers (probably not using the right words)
>>
>> I have a long data frame of >2 000 000 rows, and 6 columns. Across this
>> there are 24 000 combinations of gene in a column (n=12000) and gender in a
>> column (n=2... obviously). I want to create 2 new columns in the data frame
>> that on each row gives, in one column the mean value (of gene expression, in
>> the column called "value") for that row's gene&gender combination, and in
>> the other column the standard deviation for the gene&gender combination.
>>
>> Any suggestions?
>>
>> Rob
>>
>> Example of the top of the data frame:
>>
>> gene	variable	value	gender	line	rep
>> 1	CG10000	X208.F1.30456	4.758010	Female	208	1
>> 2	CG10000	X365.F2.30478	4.915395	Female	365	2
>> 3	CG10000	X799.F2.30509	4.641636	Female	799	2
>> 4	CG10000	X306.M2.32650	4.550676	Male	306	2
>> 5	CG10000	X712.M2.30830	4.633811	Male	712	2
>> 6	CG10000	X732.M2.30504	4.857564	Male	732	2
>> 7	CG10000	X707.F1.31120	5.104165	Female	707	1
>> 8	CG10000	X514.F2.30493	4.730814	Female	514	2
>>
>> --
>> View this message in context: http://r.789695.n4.nabble.com/Mean-of-matched-data-tp4636856.html
>> Sent from the R help mailing list archive at Nabble.com.
>>
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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.
>