[R] Converting a data frame with values into a matrix/

[John Kane]

The way that you have set up the data.frame is rather
unusual. It makes NES a factor which I suspect you
don't want. Do str(xx) to see what I mean

Here is a way that I think does what you want but with
the data.frame constructed in a different manner. 
Again do str(aa) to see the difference
=====================================================
aa <- data.frame(Name=c( "Mike" ,"Carl", "Gene",
"James","Dough"),
         Class=c(  "A",  "A",  "C",  "A",  "B"),
         NES=c( 0.01, 0.2, 0.3, -0.3, 0) )  
aa
         
library(reshape)
mm  <- melt(aa, id=c("Name", "Class"))
mm1  <- cast(mm, Class~Name)

aba <- mm1[,2:6]
aba[is.na(aba)] <- 1

final <- data.frame(mm1$Class, aba)
names(final) <- names(mm1) 
final

===================================================

--- Srinivas Iyyer <srini_iyyer_bio at yahoo.com> wrote:

> Dear Group, 
> I have a data frame like the following:
> 
> 
> x <- c("Mike","A",0.01)
> x1 <- c("Carl","A",0.2)
> x2 <- c("Gene","C",0.3)
> x3 <- c("James","A",-0.3)
> x4 <- c("Dough","B",0)
> xx <- rbind(x,x1,x2,x3,x4)
> colnames(xx)<-c("Name","Class","NES")
> xx <-as.data.frame(xx)
> 
> > xx
>     Name Class  NES
> x   Mike     A 0.01
> x1  Carl     A  0.2
> x2  Gene     C  0.3
> x3 James     A -0.3
> x4 Dough     B    0
> 
> 
> Now I want to create a matrix with unique xx$Name on
> columns and unique xx$Class as rows.  I want to fill
> my choice of values (in this case 1) if data point
> not
> available. 
> 
> 
> xy <-
>
matrix(1,length(unique(xx$Class)),length(unique(xx[,1])))
> colnames(xy)<-unique(xx[,1])
> rownames(xy)<-unique(xx$Class)
> 
> > xy
>   Mike Carl Gene James Dough
> A    1    1    1     1     1
> C    1    1    1     1     1
> B    1    1    1     1     1
> 
> 
> 
> 
> 
> I would love to have :
> 
>   Mike Carl Gene James Dough
> A    0.01    0.2    1     -0.3     1
> C    1    1    1     0.3     1
> B    1    1    1     1    0
> 
> 
> 
> 
> If I am not wrong this is called contigency or
> frequeny table. 
> 
> I tried xtabs on this.  
> 
> > z <- xtabs(NES ~ Name+Class,data=xx)
> Error in Summary.factor(4L, na.rm = FALSE) : 
>   sum not meaningful for factors
> 
> 
> I tried on other data frames, it worked. BUT the
> problem is it gives me 0.0000 even a value is not
> available for that row and column.  So if I have
> data
> -0.00 it is considered 0. 
> 
> I tried. drop.unused.levels = T, I did not get what
> I
> want. I want all row.col values not available to be
> 1.
> 
> 
> Is there any other trick where I map by row and
> column
> names instead of using advanced xtabs. 
> 
> thanks
> Srini
> 
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