library(reshape2) # you probably need to install reshape2 before this works
?melt
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Sent from my phone. Please excuse my brevity.
On May 30, 2014 3:07:25 PM PDT, Assa Yeroslaviz <fry...@gmail.com> 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.
>
>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:
> 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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