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
>
> [[alternative HTML version deleted]]
>
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David Winsemius
Alameda, CA, USA
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and provide commented, minimal, self-contained, reproducible code.
