[R] help with rowsum/aggregate type functions

[John Kane]

See the reshape package. 

library(reshape)
yy <- melt(xx, id=c("Gene.name")) 
cast(yy, Gene.name~variable, sum)

--- Charles Murtaugh <murtaugh at genetics.utah.edu>
wrote:

> Hi--
> 
>   This is a question with a trivial and obvious
> answer, I'm sure, but I can't seem to find it in the
> help files and books that I have handy.  I have a
> dataframe consisting of two columns, "Gene_Name," a
> list of gene symbols, and "Number," a numeric
> measure of how frequently a tag representing that
> gene showed up in a SAGE library.  Several of the
> genes are represented by multiple tags, and
> therefore are present more than once in the list,
> e.g.:
> 
> 1167     Zcchc8      6
> 1168     Zcwpw1      5
> 1169     Zdhhc18     6
> 1170     Zdhhc20     5
> 1171     Zdhhc3      6
> 1172     Zdhhc3      5
> 1173     Zeb2        9
> 1174     Zeb2        6
> 
>   What I want is to collapse the list by gene name,
> such that duplicates are summed up and appear only
> once in the final version:
> 
> 
> 
> Zcchc8      6
> 
> Zcwpw1      5
> 
> Zdhhc18     6
> Zdhhc20     5
> 
> Zdhhc3     11
> 
> Zeb2       15
> 
> 
> 
>   The only way I can figure out to do this is via
> rowsum:
> 
> 
> 
> > rowsum (Number,Gene_Name)
> 
> 
> 
> gives me exactly what I want, *except* that in the
> end, I am left with a matrix containing the Number
> values and with the Gene_Names used as row names
> (the output therefore looks exactly as printed
> above) -- what I want is a dataframe equivalent to
> the starting table, with numbered rows and separate,
> accessible columns containing the Gene_Name and
> Number values.
> 
> 
> 
>   I was able to put such a dataframe together
> manually, by cobbling together the row names of the
> above list with the values:
> 
> 
> 
> > genes.unique <- data.frame (rownames
> (rowsum(Number,Gene_Name)),
> rowsum(Number,Gene_Name))
> 
> 
> 
> but then I have to manually replace the row names of
> the dataframe with numbers, to get back to what I
> wanted in the first place.
> 
> 
> 
>   I hope this makes some sort of sense.  Is there an
> easier way to do this?  Thanks in advance!
> 
> 
> 
>   Charlie Murtaugh
> 
> 
> 
> 
> 
> 
> 
> =====
> 
> L. Charles Murtaugh
> Assistant Professor
> 
> University of Utah
> Dept. of Human Genetics
> 15 N. 2030 E. Rm. 2100
> Salt Lake City, UT 84112
> 
> tel 801-581-5958
> fax 801-581-6463
> email murtaugh at genetics.utah.edu
> 
> 
> 	[[alternative HTML version deleted]]
> 
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