Question

MutationalPattern R plot96 error

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khanm • 0

@khanm-20752

Last seen 5.0 years ago

I am trying to plot96 profile for this file and getting a error as listed below, any help will be greatly appreciated. thanks in advance

head(mutmat) Type X18544 X14516 X18082 X12173 X13025 X13298 X13372 X13412 X13456 X13596 1 A[C>A]A 21 19 19 29 16 22 21 15 14 19 2 A[C>A]C 18 21 12 22 14 25 13 13 9 17 3 A[C>A]G 7 9 11 12 11 17 13 20 17 11 4 A[C>A]T 12 13 18 25 9 12 10 11 9 12 5 C[C>A]A 35 47 63 59 56 63 75 89 67 62 6 C[C>A]C 46 46 55 71 28 71 96 57 58 66 plot96profile(mutmat[,c(1,5)], condensed=T) Error in sum(x) : invalid 'type' (character) of argument traceback() 3: FUN(newX[, i], ...) 2: apply(mutmatrix, 2, function(x) x/sum(x)) 1: plot96profile(mutmat[, c(1, 5)])

software error • 638 views

ADD COMMENT • link 5.0 years ago khanm • 0

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You should edit your post and clean up the code. With proper formatting, it would look like this:

> head(mutmat) 

    Type     X18544  X14516  X18082  X12173  X13025  X13298  X13372  X13412  X13456  X13596
1   A[C>A]A  21      19      19      29      16      22      21      15      14      19
2   A[C>A]C  18      21      12      22      14      25      13      13      9       17
3   A[C>A]G  7       9       11      12      11      17      13      20      17      11
4   A[C>A]T  12      13      18      25      9       12      10      11      9       12
5   C[C>A]A  35      47      63      59      56      63      75      89      67      62
6   C[C>A]C  46      46      55      71      28      71      96      57      58      66

> plot96profile(mutmat[,c(1,5)], condensed=T)

Error in sum(x) : invalid 'type' (character) of argument traceback() 3: FUN(newX[, i], ...) 2: apply(mutmatrix, 2, function(x) x/sum(x)) 1: plot96profile(mutmat[, c(1, 5)])

ADD REPLY • link 5.0 years ago Ram ▴ 190