First of all, thanks to Rolf, Brad, Robin, Erich, Fernando and Adaikalavan for your time and suggestions.
I�ve been testing some algorithms (sorry for the delay, I�m very slow, and I�m a completely beginner in R�s world).
First, the Robin algorithm.
I think that there is a problem because I�ve done 200 permutations and I�ve found that these permutations are the same:
52 and 91, 99 and 110, 121 and 122, 51 and 141, 130 and 134.
Thanks again,
Jordi Altirriba Hospital Clinic � Barcelona - Spain
x <- c(1,2,3,4,5,6,7,8,9,10,11,12) dim(x) <- c(3,4) a<-matrix(1,200,12) for (i in 1:200)
+ {
+ jj <- t(apply(x,1,sample))
+ a[i,]<-as.vector(jj)
+ }
a
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [1,] 7 2 3 1 11 6 4 8 9 10 5 12 [2,] 1 2 9 7 11 6 4 8 12 10 5 3 [3,] 7 2 9 1 11 3 4 5 6 10 8 12 [4,] 10 8 6 4 5 12 7 2 9 1 11 3 [5,] 10 2 12 1 11 9 7 8 6 4 5 3 [6,] 7 8 6 1 5 9 4 11 12 10 2 3 [7,] 1 5 12 7 2 6 4 8 9 10 11 3 [8,] 1 5 9 10 8 6 4 2 3 7 11 12 [9,] 1 11 6 7 2 12 4 5 9 10 8 3 [10,] 4 5 12 10 11 9 1 8 6 7 2 3 [11,] 1 11 9 7 5 6 4 8 12 10 2 3 [12,] 1 8 3 4 2 12 10 5 9 7 11 6 [13,] 1 2 3 7 11 6 10 5 12 4 8 9 [14,] 4 8 3 10 5 12 7 2 9 1 11 6 [15,] 10 2 3 4 8 6 7 11 9 1 5 12 [16,] 4 8 9 10 2 12 7 5 6 1 11 3 [17,] 1 2 6 10 5 3 7 8 12 4 11 9 [18,] 10 2 9 4 11 12 1 5 6 7 8 3 [19,] 4 8 6 7 11 12 1 2 9 10 5 3 [20,] 1 8 12 7 2 3 10 11 6 4 5 9 [21,] 10 2 12 1 5 9 7 11 6 4 8 3 [22,] 4 11 12 1 2 3 10 8 6 7 5 9 [23,] 1 11 3 7 2 6 10 5 9 4 8 12 [24,] 7 2 9 10 5 12 1 11 3 4 8 6 [25,] 7 8 9 1 2 6 4 5 3 10 11 12 [26,] 4 5 12 10 2 3 7 11 6 1 8 9 [27,] 4 5 9 1 11 3 7 8 12 10 2 6 [28,] 1 5 6 4 11 3 7 8 9 10 2 12 [29,] 4 5 6 1 11 9 10 2 12 7 8 3 [30,] 4 11 3 7 8 12 10 5 6 1 2 9 [31,] 10 2 3 1 11 6 7 8 9 4 5 12 [32,] 10 2 3 7 8 9 1 11 6 4 5 12 [33,] 7 11 6 1 8 9 4 5 12 10 2 3 [34,] 7 5 12 1 8 6 4 11 3 10 2 9 [35,] 1 2 3 4 8 6 7 5 9 10 11 12 [36,] 7 8 3 1 11 9 10 2 12 4 5 6 [37,] 10 2 6 1 11 12 7 5 3 4 8 9 [38,] 1 5 9 4 11 12 7 8 3 10 2 6 [39,] 1 2 12 7 5 9 10 8 3 4 11 6 [40,] 1 8 3 10 2 12 7 11 6 4 5 9 [41,] 1 2 9 4 8 3 10 11 12 7 5 6 [42,] 4 5 6 1 2 9 10 8 3 7 11 12 [43,] 1 2 6 7 11 12 10 5 9 4 8 3 [44,] 1 2 9 10 11 12 4 8 6 7 5 3 [45,] 10 5 9 7 11 6 4 2 3 1 8 12 [46,] 1 2 3 4 11 6 7 5 9 10 8 12 [47,] 4 2 6 1 8 3 10 5 12 7 11 9 [48,] 4 8 9 7 2 3 1 5 12 10 11 6 [49,] 10 8 12 1 2 9 4 11 3 7 5 6 [50,] 10 8 6 1 2 3 7 5 12 4 11 9 [51,] 7 2 12 10 11 6 4 8 3 1 5 9 [52,] 4 5 6 1 2 12 10 11 9 7 8 3 [53,] 1 2 3 7 5 6 4 8 9 10 11 12 [54,] 10 5 3 7 11 9 1 8 6 4 2 12 [55,] 7 11 12 4 2 3 10 8 6 1 5 9 [56,] 1 5 9 4 11 12 10 8 3 7 2 6 [57,] 4 5 9 7 11 3 10 2 6 1 8 12 [58,] 10 11 3 4 5 6 1 8 12 7 2 9 [59,] 4 8 9 10 5 6 7 2 3 1 11 12 [60,] 4 2 12 1 8 6 10 5 9 7 11 3 [61,] 4 8 6 7 11 9 10 5 12 1 2 3 [62,] 7 8 3 10 5 6 1 11 12 4 2 9 [63,] 10 5 3 7 8 6 1 2 9 4 11 12 [64,] 10 2 9 4 11 12 1 5 3 7 8 6 [65,] 1 11 6 4 8 12 7 2 3 10 5 9 [66,] 1 5 3 7 11 9 4 2 12 10 8 6 [67,] 4 2 6 7 5 12 10 8 9 1 11 3 [68,] 4 11 12 10 2 3 7 8 6 1 5 9 [69,] 4 5 6 10 2 3 7 8 9 1 11 12 [70,] 1 11 12 10 2 6 4 5 3 7 8 9 [71,] 10 5 6 7 8 12 4 2 9 1 11 3 [72,] 10 8 12 1 11 9 7 5 3 4 2 6 [73,] 10 8 3 7 11 9 4 5 12 1 2 6 [74,] 7 2 12 1 5 6 4 8 9 10 11 3 [75,] 7 2 12 10 8 9 1 11 6 4 5 3 [76,] 7 2 3 1 5 9 4 8 12 10 11 6 [77,] 1 11 3 10 5 6 7 2 9 4 8 12 [78,] 7 2 6 10 11 12 4 8 9 1 5 3 [79,] 10 8 6 7 5 3 1 2 9 4 11 12 [80,] 10 11 3 7 2 12 4 8 6 1 5 9 [81,] 10 5 6 1 8 3 4 11 9 7 2 12 [82,] 1 11 3 7 5 12 10 2 6 4 8 9 [83,] 4 11 9 10 5 12 7 2 6 1 8 3 [84,] 1 11 12 7 8 3 4 2 6 10 5 9 [85,] 10 2 9 7 5 6 1 11 12 4 8 3 [86,] 7 11 9 4 5 6 10 2 12 1 8 3 [87,] 4 5 12 7 2 3 10 11 6 1 8 9 [88,] 1 2 12 7 5 3 10 8 6 4 11 9 [89,] 1 8 12 7 11 9 10 2 6 4 5 3 [90,] 4 5 3 10 11 9 7 2 6 1 8 12 [91,] 4 5 6 1 2 12 10 11 9 7 8 3 [92,] 10 11 9 7 5 12 1 2 6 4 8 3 [93,] 4 2 3 7 8 6 1 11 12 10 5 9 [94,] 4 5 3 10 2 12 7 8 9 1 11 6 [95,] 4 8 3 10 11 9 1 2 6 7 5 12 [96,] 7 5 12 10 11 3 1 8 9 4 2 6 [97,] 4 2 3 1 8 6 7 11 9 10 5 12 [98,] 4 11 9 7 5 12 10 8 6 1 2 3 [99,] 1 11 12 4 5 6 7 8 3 10 2 9 [100,] 1 8 3 7 5 6 10 2 12 4 11 9 [101,] 7 11 6 4 8 3 1 2 12 10 5 9 [102,] 7 11 12 1 2 3 10 8 6 4 5 9 [103,] 4 5 12 1 2 9 7 8 3 10 11 6 [104,] 10 11 12 4 8 3 7 5 9 1 2 6 [105,] 10 5 9 1 2 3 4 8 6 7 11 12 [106,] 10 11 9 1 2 12 7 8 3 4 5 6 [107,] 10 11 3 4 8 9 7 5 12 1 2 6 [108,] 7 2 6 1 11 9 4 5 12 10 8 3 [109,] 1 8 6 7 2 12 10 5 3 4 11 9 [110,] 1 11 12 4 5 6 7 8 3 10 2 9 [111,] 7 8 6 1 5 3 10 2 12 4 11 9 [112,] 4 8 3 7 5 6 1 2 9 10 11 12 [113,] 1 2 9 4 11 6 7 5 3 10 8 12 [114,] 4 11 9 1 8 6 7 2 3 10 5 12 [115,] 10 8 3 4 11 12 7 2 9 1 5 6 [116,] 7 11 12 1 2 3 4 8 9 10 5 6 [117,] 1 5 3 10 11 12 7 8 9 4 2 6 [118,] 1 11 6 4 2 9 10 5 12 7 8 3 [119,] 10 2 3 1 5 9 4 8 12 7 11 6 [120,] 1 2 3 4 11 12 7 8 9 10 5 6 [121,] 7 8 3 4 5 12 10 2 6 1 11 9 [122,] 7 8 3 4 5 12 10 2 6 1 11 9 [123,] 4 5 3 10 11 9 7 8 6 1 2 12 [124,] 4 5 6 7 11 9 1 8 12 10 2 3 [125,] 10 8 6 1 11 9 4 2 12 7 5 3 [126,] 10 8 12 4 11 9 7 2 6 1 5 3 [127,] 7 8 12 1 11 6 10 5 9 4 2 3 [128,] 1 8 12 10 11 3 7 5 9 4 2 6 [129,] 7 8 3 10 2 6 1 11 9 4 5 12 [130,] 7 11 9 1 2 6 10 8 3 4 5 12 [131,] 10 2 3 4 11 9 1 5 6 7 8 12 [132,] 4 11 3 1 5 9 10 2 6 7 8 12 [133,] 10 2 12 7 8 3 4 5 6 1 11 9 [134,] 7 11 9 1 2 6 10 8 3 4 5 12 [135,] 7 8 3 4 11 6 10 2 9 1 5 12 [136,] 10 8 9 7 11 12 1 2 6 4 5 3 [137,] 10 8 12 4 5 3 1 2 9 7 11 6 [138,] 1 2 6 10 8 12 7 11 9 4 5 3 [139,] 4 5 3 7 11 9 1 2 12 10 8 6 [140,] 4 5 12 7 8 6 10 11 3 1 2 9 [141,] 7 2 12 10 11 6 4 8 3 1 5 9 [142,] 10 11 12 7 2 6 1 5 3 4 8 9 [143,] 7 2 3 10 11 6 1 8 9 4 5 12 [144,] 1 2 9 10 5 12 4 8 3 7 11 6 [145,] 1 11 6 4 8 9 7 5 12 10 2 3 [146,] 4 5 3 10 2 6 1 11 9 7 8 12 [147,] 7 11 9 1 2 3 10 8 12 4 5 6 [148,] 4 2 3 1 5 12 7 8 6 10 11 9 [149,] 10 11 12 4 8 3 1 2 9 7 5 6 [150,] 4 8 3 10 5 6 1 11 9 7 2 12 [151,] 1 8 6 10 5 9 4 11 3 7 2 12 [152,] 4 8 6 7 11 12 10 5 3 1 2 9 [153,] 7 2 3 10 5 6 4 11 9 1 8 12 [154,] 10 5 12 1 8 9 7 2 3 4 11 6 [155,] 1 8 6 4 2 9 10 5 3 7 11 12 [156,] 10 2 3 7 5 9 4 11 12 1 8 6 [157,] 10 5 3 1 2 6 7 8 9 4 11 12 [158,] 7 11 12 4 5 9 10 8 3 1 2 6 [159,] 7 5 3 1 8 12 10 2 6 4 11 9 [160,] 7 2 6 4 11 3 1 5 12 10 8 9 [161,] 7 5 3 1 2 12 4 8 9 10 11 6 [162,] 7 8 12 1 5 6 10 11 9 4 2 3 [163,] 10 11 9 4 8 6 1 2 3 7 5 12 [164,] 7 11 6 1 5 9 4 2 12 10 8 3 [165,] 4 11 9 10 8 3 7 2 12 1 5 6 [166,] 4 2 6 10 8 9 7 11 12 1 5 3 [167,] 7 5 3 10 2 12 4 8 6 1 11 9 [168,] 1 8 12 7 2 3 4 5 9 10 11 6 [169,] 7 8 12 1 5 6 4 2 3 10 11 9 [170,] 4 5 3 7 8 9 1 2 12 10 11 6 [171,] 7 11 9 1 8 6 4 2 12 10 5 3 [172,] 10 8 3 1 2 9 4 11 12 7 5 6 [173,] 10 5 12 7 8 9 4 11 3 1 2 6 [174,] 10 11 6 7 5 3 4 8 12 1 2 9 [175,] 7 11 12 1 2 3 10 8 9 4 5 6 [176,] 1 11 12 7 2 3 4 8 9 10 5 6 [177,] 10 11 12 4 5 3 7 8 6 1 2 9 [178,] 10 5 3 7 2 6 4 8 12 1 11 9 [179,] 1 5 6 7 2 9 10 11 3 4 8 12 [180,] 1 11 12 10 5 6 4 2 3 7 8 9 [181,] 7 2 12 4 11 9 1 5 6 10 8 3 [182,] 10 11 12 1 5 3 7 8 9 4 2 6 [183,] 4 8 3 1 11 9 7 2 6 10 5 12 [184,] 4 8 9 7 2 3 10 5 6 1 11 12 [185,] 10 11 9 1 5 6 7 2 12 4 8 3 [186,] 10 5 12 4 8 9 7 2 6 1 11 3 [187,] 4 2 3 1 8 6 7 5 12 10 11 9 [188,] 10 2 9 4 11 12 1 8 3 7 5 6 [189,] 10 2 12 7 11 3 4 5 9 1 8 6 [190,] 4 5 6 7 8 3 10 11 9 1 2 12 [191,] 10 5 9 1 2 3 7 11 12 4 8 6 [192,] 4 11 9 7 2 6 10 5 3 1 8 12 [193,] 10 11 12 1 2 6 4 5 9 7 8 3 [194,] 10 2 3 4 11 12 7 5 6 1 8 9 [195,] 4 2 6 7 8 9 1 11 3 10 5 12 [196,] 10 2 12 4 8 6 7 5 3 1 11 9 [197,] 7 5 12 4 11 9 1 2 3 10 8 6 [198,] 10 5 6 1 11 3 7 2 9 4 8 12 [199,] 1 2 9 7 11 3 4 8 6 10 5 12 [200,] 4 8 3 7 11 12 1 2 6 10 5 9
From: Robin Hankin <[EMAIL PROTECTED]> To: Jordi Altirriba Guti�rrez <[EMAIL PROTECTED]> CC: [EMAIL PROTECTED] Subject: Re: [R] (no subject) (was: Permutations) Date: Wed, 14 Jul 2004 09:11:48 +0100
Jordi
try this
R> x <- c(1,2,3, 10,11,12, 41,42,43, 81,82,83) R> dim(x) <- c(3,4) R> x [,1] [,2] [,3] [,4] [1,] 1 10 41 81 [2,] 2 11 42 82 [3,] 3 12 43 83 R> jj <- t(apply(x,1,sample)) R> jj [,1] [,2] [,3] [,4] [1,] 1 41 10 81 [2,] 2 11 82 42 [3,] 12 3 43 83 R> as.vector(jj) R> [1] 1 2 12 41 11 3 10 82 43 81 42 83
and I think that does what you want...
We take the vector, rearrange it into a matrix with three rows, then sample *within* the rows,
then rearrange into a vector again.
There will be one forbidden permutation, namely the identity (which may or may not be
desirable).
This method doesn't allow "intra block" permutations.
best
rksh
Dear R users,
First of all, thanks for the incredibly fast answers and help of Rolf, Marc and Robert.
Yes, I noticed that it was a lot of permutacions, but my intention was to make this process automatic and take only 5.000 - 10.000 permutations. Therefore, I wanted only to take that "interesting permutations" with "some information" [inter-block permutations].
The reason why I'm interested in these permutations is because I'm using some packages of Bioconductor to analyse my data from some microarrays and I thought that perhaps could be interesting to see what happens when I permute my data and I compare it against the not permuted data.
Thanks again for your time and suggestions.
Jordi Altirriba Ph. D. Student
Hospital Clinic-Barcelona-Spain
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