[R] converting a data.frame into a different table

[David Winsemius]

On May 30, 2014, at 3:07 PM, Assa Yeroslaviz wrote:

> Hi,
> 
> I have a matrix of 4.5Kx4.5K elements with column- and row names
> 
> I need to convert this matrix into a table, where one column is the name of
> the row for the element, the second column is the name of the column for
> the same element and the third column is the element itself.

In R a "table" object is just a matrix with a class of table and there is a really kewl function to do exactly what you ask for on objects with class table so try this:

class(out5.df) <- "table"

my.df <- as.data.frame(out5.df)

> 
> The way I do it at the moment is with a double for-loop.
> With this way though it takes ages for the loop to finish.
> 
> I was wondering whether there is a faster way of doing the same conversion.
> 
> This is how I am doing it now:
> my.df <-data.frame()
> for (i in 1:(nrow(out5.df)-1)){
>    for (j in i:ncol(out5.df)) {
> #        print(paste(" I am at position: row-", i, " and col-", j, sep=""))
>        a<- cbind(start=rownames(out5.df)[i], start.1=colnames(out5.df)[j],
> Value=out5.df[i,j])
>        my.df <- rbind(my.df, a)
>        }
>    }
> 
> this is an example for the data I have:

I would have tested this if it had been offered using the output of dput()

?dput


> out5.df <- matrix(1:30,5,6)
> colnames(out5.df)<-letters[1:6]
> rownames(out5.df)<-LETTERS[1:5]
> class(out5.df) <- "table"
> 
> my.df <- as.data.frame(out5.df)
> 
> my.df
   Var1 Var2 Freq
1     A    a    1
2     B    a    2
3     C    a    3
4     D    a    4
5     E    a    5
6     A    b    6
.......snippped the rest

-- 
David.
> 


>    1    2    3    4    5    6    7
> 1    FBgn0037249    FBpp0312226    FBtr0346646    FBgn0266186
> FBpp0312219    FBtr0346639    FBgn0010100
> 2    FBgn0036389    FBpp0312225    FBtr0346645    FBgn0037894
> FBpp0312218    FBtr0346638    FBgn0026577
> 3    FBgn0014002    FBpp0312224    FBtr0346644    FBgn0025712
> FBpp0312183    FBtr0346593    FBpp0312178
> 4    FBgn0034201    FBpp0312223    FBtr0346643    FBgn0025712
> FBpp0312182    FBtr0346592    FBpp0312177
> 5    FBgn0029860    FBpp0312222    FBtr0346642    FBgn0261597
> FBpp0312181    FBtr0346591    FBtr0346587
> 6    FBgn0028526    FBpp0312221    FBtr0346641    FBgn0263050
> FBpp0312180    FBtr0346589    FBtr0346586
> 7    FBgn0003486    FBpp0312220    FBtr0346640    FBgn0263051
> FBpp0312179    FBtr0346588    FBpp0312219
> 
> What I would like to get at the end is something like that:
>> my.df
>   start start.1       Value
> 1      1      X1 FBgn0037249
> 2      1      X2 FBpp0312226
> 3      1      X3 FBtr0346646
> 4      1      X4 FBgn0266186
> 5      1      X5 FBpp0312219
> 6      1      X6 FBtr0346639
> 7      1      X7 FBgn0010100
> 8      2      X2 FBpp0312225
> 9      2      X3 FBtr0346645
> 10     2      X4 FBgn0037894
> 11     2      X5 FBpp0312218
> 12     2      X6 FBtr0346638
> 13     2      X7 FBgn0026577
> 14     3      X3 FBtr0346644
> 15     3      X4 FBgn0025712
> 16     3      X5 FBpp0312183
> 17     3      X6 FBtr0346593
> 18     3      X7 FBpp0312178
> 19     4      X4 FBgn0025712
> 20     4      X5 FBpp0312182
> 21     4      X6 FBtr0346592
> 22     4      X7 FBpp0312177
> 23     5      X5 FBpp0312181
> 24     5      X6 FBtr0346591
> 25     5      X7 FBtr0346587
> 26     6      X6 FBtr0346589
> 27     6      X7 FBtr0346586
> 
> 
> Sp I would like to know if there is a better way of ding it than a double
> for loop.
> 
> thanks
> Assa
> 
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> 
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David Winsemius
Alameda, CA, USA